data_3UD4 # _entry.id 3UD4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3UD4 pdb_00003ud4 10.2210/pdb3ud4/pdb NDB NA1368 ? ? RCSB RCSB068603 ? ? WWPDB D_1000068603 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3UCU . unspecified PDB 3UCZ . unspecified PDB 3UD3 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3UD4 _pdbx_database_status.recvd_initial_deposition_date 2011-10-27 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Smith, K.D.' 1 'Strobel, S.A.' 2 # _citation.id primary _citation.title 'Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer.' _citation.journal_abbrev Biochemistry _citation.journal_volume 51 _citation.page_first 425 _citation.page_last 432 _citation.year 2012 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22148472 _citation.pdbx_database_id_DOI 10.1021/bi2016662 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Smith, K.D.' 1 ? primary 'Lipchock, S.V.' 2 ? primary 'Strobel, S.A.' 3 ? # _cell.entry_id 3UD4 _cell.length_a 49.612 _cell.length_b 45.116 _cell.length_c 76.049 _cell.angle_alpha 90.00 _cell.angle_beta 96.05 _cell.angle_gamma 90.00 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3UD4 _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'U1 small nuclear ribonucleoprotein A' 11340.315 1 ? 'Y31H, Q36R' 'RNA binding domain, UNP residues 1-98' ? 2 polymer syn 'RNA (92-MER)' 29943.758 1 ? ? ? 'c-di-GMP-I riboswitch' 3 polymer syn ;RNA (5'-R(*GP*A)-3') ; 629.454 1 ? ? ? GpA 4 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 5 water nat water 18.015 11 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'U1 snRNP A, U1-A, U1A' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;MAVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK PMRIQYAKTDSDIIAKMK ; ;MAVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK PMRIQYAKTDSDIIAKMK ; P ? 2 polyribonucleotide no yes ;(GTP)GUCACGCACAGGGCAAACCAUUCGAAAGAGUGGGACGCAAAGCCUCCGGCCUAAACCAUUGCACUCCGGUAGGUA GCGGGGUUAUCGAUGG ; ;GGUCACGCACAGGGCAAACCAUUCGAAAGAGUGGGACGCAAAGCCUCCGGCCUAAACCAUUGCACUCCGGUAGGUAGCGG GGUUAUCGAUGG ; R ? 3 polyribonucleotide no no GA GA B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 ALA n 1 3 VAL n 1 4 PRO n 1 5 GLU n 1 6 THR n 1 7 ARG n 1 8 PRO n 1 9 ASN n 1 10 HIS n 1 11 THR n 1 12 ILE n 1 13 TYR n 1 14 ILE n 1 15 ASN n 1 16 ASN n 1 17 LEU n 1 18 ASN n 1 19 GLU n 1 20 LYS n 1 21 ILE n 1 22 LYS n 1 23 LYS n 1 24 ASP n 1 25 GLU n 1 26 LEU n 1 27 LYS n 1 28 LYS n 1 29 SER n 1 30 LEU n 1 31 HIS n 1 32 ALA n 1 33 ILE n 1 34 PHE n 1 35 SER n 1 36 ARG n 1 37 PHE n 1 38 GLY n 1 39 GLN n 1 40 ILE n 1 41 LEU n 1 42 ASP n 1 43 ILE n 1 44 LEU n 1 45 VAL n 1 46 SER n 1 47 ARG n 1 48 SER n 1 49 LEU n 1 50 LYS n 1 51 MET n 1 52 ARG n 1 53 GLY n 1 54 GLN n 1 55 ALA n 1 56 PHE n 1 57 VAL n 1 58 ILE n 1 59 PHE n 1 60 LYS n 1 61 GLU n 1 62 VAL n 1 63 SER n 1 64 SER n 1 65 ALA n 1 66 THR n 1 67 ASN n 1 68 ALA n 1 69 LEU n 1 70 ARG n 1 71 SER n 1 72 MET n 1 73 GLN n 1 74 GLY n 1 75 PHE n 1 76 PRO n 1 77 PHE n 1 78 TYR n 1 79 ASP n 1 80 LYS n 1 81 PRO n 1 82 MET n 1 83 ARG n 1 84 ILE n 1 85 GLN n 1 86 TYR n 1 87 ALA n 1 88 LYS n 1 89 THR n 1 90 ASP n 1 91 SER n 1 92 ASP n 1 93 ILE n 1 94 ILE n 1 95 ALA n 1 96 LYS n 1 97 MET n 1 98 LYS n 2 1 GTP n 2 2 G n 2 3 U n 2 4 C n 2 5 A n 2 6 C n 2 7 G n 2 8 C n 2 9 A n 2 10 C n 2 11 A n 2 12 G n 2 13 G n 2 14 G n 2 15 C n 2 16 A n 2 17 A n 2 18 A n 2 19 C n 2 20 C n 2 21 A n 2 22 U n 2 23 U n 2 24 C n 2 25 G n 2 26 A n 2 27 A n 2 28 A n 2 29 G n 2 30 A n 2 31 G n 2 32 U n 2 33 G n 2 34 G n 2 35 G n 2 36 A n 2 37 C n 2 38 G n 2 39 C n 2 40 A n 2 41 A n 2 42 A n 2 43 G n 2 44 C n 2 45 C n 2 46 U n 2 47 C n 2 48 C n 2 49 G n 2 50 G n 2 51 C n 2 52 C n 2 53 U n 2 54 A n 2 55 A n 2 56 A n 2 57 C n 2 58 C n 2 59 A n 2 60 U n 2 61 U n 2 62 G n 2 63 C n 2 64 A n 2 65 C n 2 66 U n 2 67 C n 2 68 C n 2 69 G n 2 70 G n 2 71 U n 2 72 A n 2 73 G n 2 74 G n 2 75 U n 2 76 A n 2 77 G n 2 78 C n 2 79 G n 2 80 G n 2 81 G n 2 82 G n 2 83 U n 2 84 U n 2 85 A n 2 86 U n 2 87 C n 2 88 G n 2 89 A n 2 90 U n 2 91 G n 2 92 G n 3 1 G n 3 2 A n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene SNRPA _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 511693 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain BL21 _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET11 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _pdbx_entity_src_syn.entity_id 2 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'in vitro transcribed RNA transcript' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP SNRPA_HUMAN P09012 1 ;MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK PMRIQYAKTDSDIIAKMK ; 1 ? 2 PDB 3UD4 3UD4 2 ? ? ? 3 PDB 3UD4 3UD4 3 ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3UD4 P 1 ? 98 ? P09012 1 ? 98 ? 1 98 2 2 3UD4 R 1 ? 92 ? 3UD4 8 ? 98 ? 8 98 3 3 3UD4 B 1 ? 2 ? 3UD4 1 ? 2 ? 1 2 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3UD4 HIS P 31 ? UNP P09012 TYR 31 'engineered mutation' 31 1 1 3UD4 ARG P 36 ? UNP P09012 GLN 36 'engineered mutation' 36 2 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3UD4 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.02 _exptl_crystal.density_percent_sol 39.09 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_details '24% PEG550mme, 50 mM MES, pH 6.0, 5 mM MgSO4, 300 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2010-04-29 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X25' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X25 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.1 # _reflns.entry_id 3UD4 _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.7 _reflns.number_obs 9365 _reflns.number_all 9403 _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.083 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 15.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.70 _reflns_shell.d_res_low 2.75 _reflns_shell.percent_possible_all 99.8 _reflns_shell.Rmerge_I_obs 0.63 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.9 _reflns_shell.pdbx_redundancy 3.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3UD4 _refine.ls_number_reflns_obs 8878 _refine.ls_number_reflns_all 8878 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 50 _refine.ls_d_res_high 2.70 _refine.ls_percent_reflns_obs 98.79 _refine.ls_R_factor_obs 0.22460 _refine.ls_R_factor_all 0.22460 _refine.ls_R_factor_R_work 0.22155 _refine.ls_R_factor_R_free 0.29041 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 445 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.921 _refine.correlation_coeff_Fo_to_Fc_free 0.798 _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'PDB entry 3MXH' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free 0.445 _refine.overall_SU_ML 0.364 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 712 _refine_hist.pdbx_number_atoms_nucleic_acid 2026 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 2750 _refine_hist.d_res_high 2.70 _refine_hist.d_res_low 50 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.005 0.021 ? 2997 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.123 2.775 ? 4517 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 5.728 5.000 ? 86 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 38.147 23.235 ? 34 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 18.099 15.000 ? 144 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 15.134 15.000 ? 6 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.003 0.020 ? 1518 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.697 _refine_ls_shell.d_res_low 2.767 _refine_ls_shell.number_reflns_R_work 615 _refine_ls_shell.R_factor_R_work 0.412 _refine_ls_shell.percent_reflns_obs 93.38 _refine_ls_shell.R_factor_R_free 0.360 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 34 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 615 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3UD4 _struct.title 'The C92U mutant c-di-GMP-I riboswitch bound to GpA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3UD4 _struct_keywords.pdbx_keywords 'SIGNALING PROTEIN/RNA' _struct_keywords.text 'riboswitch, SIGNALING PROTEIN-RNA complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 5 ? G N N 5 ? # _struct_biol.id 1 _struct_biol.details 'THE PROTEIN IS NOT BIOLOGICALLY RELEVANT AND HAS BEEN USED AS A CRYSTALLIZATION CHAPERONE.' # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 LYS A 22 ? SER A 35 ? LYS P 22 SER P 35 1 ? 14 HELX_P HELX_P2 2 ARG A 36 ? GLY A 38 ? ARG P 36 GLY P 38 5 ? 3 HELX_P HELX_P3 3 GLU A 61 ? GLN A 73 ? GLU P 61 GLN P 73 1 ? 13 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? B GTP 1 "O3'" ? ? ? 1_555 B G 2 P ? ? R GTP 8 R G 9 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale2 covale both ? B C 58 "O3'" ? ? ? 1_555 B A 59 P ? ? R C 65 R A 660 1_555 ? ? ? ? ? ? ? 1.604 ? ? metalc1 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? P MG 99 P HOH 101 1_555 ? ? ? ? ? ? ? 2.174 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? P MG 99 P HOH 102 1_555 ? ? ? ? ? ? ? 2.165 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? P MG 99 P HOH 103 1_555 ? ? ? ? ? ? ? 2.165 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? P MG 99 P HOH 104 1_555 ? ? ? ? ? ? ? 2.177 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? P MG 99 P HOH 105 1_555 ? ? ? ? ? ? ? 2.178 ? ? hydrog1 hydrog ? ? B C 4 N3 ? ? ? 1_555 B G 92 N1 ? ? R C 11 R G 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? B C 4 N4 ? ? ? 1_555 B G 92 O6 ? ? R C 11 R G 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? B C 4 O2 ? ? ? 1_555 B G 92 N2 ? ? R C 11 R G 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? B A 5 N1 ? ? ? 1_555 B G 91 N1 ? ? R A 12 R G 97 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog5 hydrog ? ? B A 5 N6 ? ? ? 1_555 B G 91 O6 ? ? R A 12 R G 97 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog6 hydrog ? ? B C 6 N3 ? ? ? 1_555 B G 88 N1 ? ? R C 13 R G 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? B C 6 N4 ? ? ? 1_555 B G 88 O6 ? ? R C 13 R G 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? B C 6 O2 ? ? ? 1_555 B G 88 N2 ? ? R C 13 R G 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? B G 7 N2 ? ? ? 1_555 B A 9 N7 ? ? R G 14 R A 16 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog10 hydrog ? ? B G 7 N1 ? ? ? 1_555 B C 87 N3 ? ? R G 14 R C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? B G 7 N2 ? ? ? 1_555 B C 87 O2 ? ? R G 14 R C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? B G 7 O6 ? ? ? 1_555 B C 87 N4 ? ? R G 14 R C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B G 7 N3 ? ? ? 1_555 B A 89 N6 ? ? R G 14 R A 95 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog14 hydrog ? ? B A 9 N6 ? ? ? 1_555 B C 87 O2 ? ? R A 16 R C 93 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog15 hydrog ? ? B C 10 N4 ? ? ? 1_555 B C 87 O2 ? ? R C 17 R C 93 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog16 hydrog ? ? B C 10 N4 ? ? ? 1_555 C A 2 N3 ? ? R C 17 B A 2 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog17 hydrog ? ? B A 11 N6 ? ? ? 1_555 B U 86 O2 ? ? R A 18 R U 92 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog18 hydrog ? ? B G 12 O6 ? ? ? 1_555 B A 40 N6 ? ? R G 19 R A 47 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog19 hydrog ? ? B G 13 N1 ? ? ? 1_555 C G 1 N7 ? ? R G 20 B G 1 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog20 hydrog ? ? B G 13 N2 ? ? ? 1_555 C G 1 O6 ? ? R G 20 B G 1 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog21 hydrog ? ? B G 14 N1 ? ? ? 1_555 B C 39 N3 ? ? R G 21 R C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B G 14 N2 ? ? ? 1_555 B C 39 O2 ? ? R G 21 R C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B G 14 O6 ? ? ? 1_555 B C 39 N4 ? ? R G 21 R C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B C 15 N3 ? ? ? 1_555 B G 38 N1 ? ? R C 22 R G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B C 15 N4 ? ? ? 1_555 B G 38 O6 ? ? R C 22 R G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B C 15 O2 ? ? ? 1_555 B G 38 N2 ? ? R C 22 R G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B A 16 N3 ? ? ? 1_555 B C 37 N4 ? ? R A 23 R C 44 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog28 hydrog ? ? B A 18 N6 ? ? ? 1_555 B G 35 N3 ? ? R A 25 R G 42 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog29 hydrog ? ? B A 18 N7 ? ? ? 1_555 B G 35 N2 ? ? R A 25 R G 42 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog30 hydrog ? ? B C 19 N3 ? ? ? 1_555 B G 34 N1 ? ? R C 26 R G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 19 N4 ? ? ? 1_555 B G 34 O6 ? ? R C 26 R G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 19 O2 ? ? ? 1_555 B G 34 N2 ? ? R C 26 R G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B C 20 N3 ? ? ? 1_555 B G 33 N1 ? ? R C 27 R G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B C 20 N4 ? ? ? 1_555 B G 33 O6 ? ? R C 27 R G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B C 20 O2 ? ? ? 1_555 B G 33 N2 ? ? R C 27 R G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B A 21 N1 ? ? ? 1_555 B U 32 N3 ? ? R A 28 R U 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B A 21 N6 ? ? ? 1_555 B U 32 O4 ? ? R A 28 R U 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B U 22 N3 ? ? ? 1_555 B G 31 O6 ? ? R U 29 R G 38 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog39 hydrog ? ? B U 22 O2 ? ? ? 1_555 B G 31 N1 ? ? R U 29 R G 38 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog40 hydrog ? ? B U 23 N3 ? ? ? 1_555 B A 30 N1 ? ? R U 30 R A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B U 23 O4 ? ? ? 1_555 B A 30 N6 ? ? R U 30 R A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B C 24 N3 ? ? ? 1_555 B G 29 N1 ? ? R C 31 R G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B C 24 N4 ? ? ? 1_555 B G 29 O6 ? ? R C 31 R G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B C 24 O2 ? ? ? 1_555 B G 29 N2 ? ? R C 31 R G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? B G 25 N2 ? ? ? 1_555 B A 28 N7 ? ? R G 32 R A 35 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog46 hydrog ? ? B A 28 N3 ? ? ? 1_555 B G 73 N2 ? ? R A 35 R G 79 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog47 hydrog ? ? B C 37 N3 ? ? ? 1_555 B G 77 N1 ? ? R C 44 R G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? B C 37 N4 ? ? ? 1_555 B G 77 O6 ? ? R C 44 R G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? B C 37 O2 ? ? ? 1_555 B G 77 N2 ? ? R C 44 R G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? B G 38 N2 ? ? ? 1_555 B A 42 N3 ? ? R G 45 R A 49 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog51 hydrog ? ? B A 41 N6 ? ? ? 1_555 B U 84 O2 ? ? R A 48 R U 90 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog52 hydrog ? ? B A 41 N7 ? ? ? 1_555 B U 84 N3 ? ? R A 48 R U 90 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog53 hydrog ? ? B G 43 N1 ? ? ? 1_555 B U 83 O2 ? ? R G 50 R U 89 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog54 hydrog ? ? B G 43 O6 ? ? ? 1_555 B U 83 N3 ? ? R G 50 R U 89 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog55 hydrog ? ? B C 44 N3 ? ? ? 1_555 B G 82 N1 ? ? R C 51 R G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B C 44 N4 ? ? ? 1_555 B G 82 O6 ? ? R C 51 R G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B C 44 O2 ? ? ? 1_555 B G 82 N2 ? ? R C 51 R G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B C 45 N3 ? ? ? 1_555 B G 81 N1 ? ? R C 52 R G 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B C 45 N4 ? ? ? 1_555 B G 81 O6 ? ? R C 52 R G 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? B C 45 O2 ? ? ? 1_555 B G 81 N2 ? ? R C 52 R G 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B U 46 O2 ? ? ? 1_555 B C 48 N4 ? ? R U 53 R C 55 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog62 hydrog ? ? B C 47 N4 ? ? ? 1_555 B A 76 N1 ? ? R C 54 R A 82 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog63 hydrog ? ? B C 47 N3 ? ? ? 1_555 B G 80 N1 ? ? R C 54 R G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? B C 47 N4 ? ? ? 1_555 B G 80 O6 ? ? R C 54 R G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? B C 47 O2 ? ? ? 1_555 B G 80 N2 ? ? R C 54 R G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? B C 48 N3 ? ? ? 1_555 B G 79 N1 ? ? R C 55 R G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? B C 48 N4 ? ? ? 1_555 B G 79 O6 ? ? R C 55 R G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? B C 48 O2 ? ? ? 1_555 B G 79 N2 ? ? R C 55 R G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? B G 49 N1 ? ? ? 1_555 B C 78 N3 ? ? R G 56 R C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? B G 49 N2 ? ? ? 1_555 B C 78 O2 ? ? R G 56 R C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? B G 49 O6 ? ? ? 1_555 B C 78 N4 ? ? R G 56 R C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? B G 50 N1 ? ? ? 1_555 B U 75 O2 ? ? R G 57 R U 81 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog73 hydrog ? ? B G 50 O6 ? ? ? 1_555 B U 75 N3 ? ? R G 57 R U 81 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog74 hydrog ? ? B C 51 N3 ? ? ? 1_555 B G 74 N1 ? ? R C 58 R G 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? B C 51 N4 ? ? ? 1_555 B G 74 O6 ? ? R C 58 R G 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? B C 51 O2 ? ? ? 1_555 B G 74 N2 ? ? R C 58 R G 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? B C 52 N3 ? ? ? 1_555 B G 73 N1 ? ? R C 59 R G 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? B C 52 N4 ? ? ? 1_555 B G 73 O6 ? ? R C 59 R G 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? B C 52 O2 ? ? ? 1_555 B G 73 N2 ? ? R C 59 R G 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? B U 53 N3 ? ? ? 1_555 B A 72 N1 ? ? R U 60 R A 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? B U 53 O4 ? ? ? 1_555 B A 72 N6 ? ? R U 60 R A 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? B A 56 N6 ? ? ? 1_555 B U 71 O2 ? ? R A 63 R U 77 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog83 hydrog ? ? B C 57 N3 ? ? ? 1_555 B G 70 N1 ? ? R C 64 R G 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? B C 57 N4 ? ? ? 1_555 B G 70 O6 ? ? R C 64 R G 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? B C 57 O2 ? ? ? 1_555 B G 70 N2 ? ? R C 64 R G 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? B C 58 N3 ? ? ? 1_555 B G 69 N1 ? ? R C 65 R G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? B C 58 N4 ? ? ? 1_555 B G 69 O6 ? ? R C 65 R G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? B C 58 O2 ? ? ? 1_555 B G 69 N2 ? ? R C 65 R G 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? B U 86 N3 ? ? ? 1_555 C A 2 N1 ? ? R U 92 B A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? B U 86 O4 ? ? ? 1_555 C A 2 N6 ? ? R U 92 B A 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ILE A 40 ? LEU A 44 ? ILE P 40 LEU P 44 A 2 ALA A 55 ? PHE A 59 ? ALA P 55 PHE P 59 A 3 THR A 11 ? ASN A 15 ? THR P 11 ASN P 15 A 4 ARG A 83 ? TYR A 86 ? ARG P 83 TYR P 86 B 1 PRO A 76 ? PHE A 77 ? PRO P 76 PHE P 77 B 2 LYS A 80 ? PRO A 81 ? LYS P 80 PRO P 81 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N LEU A 41 ? N LEU P 41 O ILE A 58 ? O ILE P 58 A 2 3 O ALA A 55 ? O ALA P 55 N ILE A 14 ? N ILE P 14 A 3 4 N ASN A 15 ? N ASN P 15 O ARG A 83 ? O ARG P 83 B 1 2 N PHE A 77 ? N PHE P 77 O LYS A 80 ? O LYS P 80 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id P _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 99 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE MG P 99' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 HIS A 31 ? HIS P 31 . ? 1_555 ? 2 AC1 6 HOH E . ? HOH P 101 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH P 102 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH P 103 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH P 104 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH P 105 . ? 1_555 ? # _database_PDB_matrix.entry_id 3UD4 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3UD4 _atom_sites.fract_transf_matrix[1][1] 0.020156 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.002137 _atom_sites.fract_transf_matrix[2][1] -0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022165 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] -0.000000 _atom_sites.fract_transf_matrix[3][3] 0.013223 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 ? ? ? P . n A 1 2 ALA 2 2 ? ? ? P . n A 1 3 VAL 3 3 ? ? ? P . n A 1 4 PRO 4 4 ? ? ? P . n A 1 5 GLU 5 5 ? ? ? P . n A 1 6 THR 6 6 ? ? ? P . n A 1 7 ARG 7 7 7 ARG ARG P . n A 1 8 PRO 8 8 8 PRO PRO P . n A 1 9 ASN 9 9 9 ASN ASN P . n A 1 10 HIS 10 10 10 HIS HIS P . n A 1 11 THR 11 11 11 THR THR P . n A 1 12 ILE 12 12 12 ILE ILE P . n A 1 13 TYR 13 13 13 TYR TYR P . n A 1 14 ILE 14 14 14 ILE ILE P . n A 1 15 ASN 15 15 15 ASN ASN P . n A 1 16 ASN 16 16 16 ASN ASN P . n A 1 17 LEU 17 17 17 LEU LEU P . n A 1 18 ASN 18 18 18 ASN ASN P . n A 1 19 GLU 19 19 19 GLU GLU P . n A 1 20 LYS 20 20 20 LYS LYS P . n A 1 21 ILE 21 21 21 ILE ILE P . n A 1 22 LYS 22 22 22 LYS LYS P . n A 1 23 LYS 23 23 23 LYS LYS P . n A 1 24 ASP 24 24 24 ASP ASP P . n A 1 25 GLU 25 25 25 GLU GLU P . n A 1 26 LEU 26 26 26 LEU LEU P . n A 1 27 LYS 27 27 27 LYS LYS P . n A 1 28 LYS 28 28 28 LYS LYS P . n A 1 29 SER 29 29 29 SER SER P . n A 1 30 LEU 30 30 30 LEU LEU P . n A 1 31 HIS 31 31 31 HIS HIS P . n A 1 32 ALA 32 32 32 ALA ALA P . n A 1 33 ILE 33 33 33 ILE ILE P . n A 1 34 PHE 34 34 34 PHE PHE P . n A 1 35 SER 35 35 35 SER SER P . n A 1 36 ARG 36 36 36 ARG ARG P . n A 1 37 PHE 37 37 37 PHE PHE P . n A 1 38 GLY 38 38 38 GLY GLY P . n A 1 39 GLN 39 39 39 GLN GLN P . n A 1 40 ILE 40 40 40 ILE ILE P . n A 1 41 LEU 41 41 41 LEU LEU P . n A 1 42 ASP 42 42 42 ASP ASP P . n A 1 43 ILE 43 43 43 ILE ILE P . n A 1 44 LEU 44 44 44 LEU LEU P . n A 1 45 VAL 45 45 45 VAL VAL P . n A 1 46 SER 46 46 46 SER SER P . n A 1 47 ARG 47 47 47 ARG ARG P . n A 1 48 SER 48 48 48 SER SER P . n A 1 49 LEU 49 49 49 LEU LEU P . n A 1 50 LYS 50 50 50 LYS LYS P . n A 1 51 MET 51 51 51 MET MET P . n A 1 52 ARG 52 52 52 ARG ARG P . n A 1 53 GLY 53 53 53 GLY GLY P . n A 1 54 GLN 54 54 54 GLN GLN P . n A 1 55 ALA 55 55 55 ALA ALA P . n A 1 56 PHE 56 56 56 PHE PHE P . n A 1 57 VAL 57 57 57 VAL VAL P . n A 1 58 ILE 58 58 58 ILE ILE P . n A 1 59 PHE 59 59 59 PHE PHE P . n A 1 60 LYS 60 60 60 LYS LYS P . n A 1 61 GLU 61 61 61 GLU GLU P . n A 1 62 VAL 62 62 62 VAL VAL P . n A 1 63 SER 63 63 63 SER SER P . n A 1 64 SER 64 64 64 SER SER P . n A 1 65 ALA 65 65 65 ALA ALA P . n A 1 66 THR 66 66 66 THR THR P . n A 1 67 ASN 67 67 67 ASN ASN P . n A 1 68 ALA 68 68 68 ALA ALA P . n A 1 69 LEU 69 69 69 LEU LEU P . n A 1 70 ARG 70 70 70 ARG ARG P . n A 1 71 SER 71 71 71 SER SER P . n A 1 72 MET 72 72 72 MET MET P . n A 1 73 GLN 73 73 73 GLN GLN P . n A 1 74 GLY 74 74 74 GLY GLY P . n A 1 75 PHE 75 75 75 PHE PHE P . n A 1 76 PRO 76 76 76 PRO PRO P . n A 1 77 PHE 77 77 77 PHE PHE P . n A 1 78 TYR 78 78 78 TYR TYR P . n A 1 79 ASP 79 79 79 ASP ASP P . n A 1 80 LYS 80 80 80 LYS LYS P . n A 1 81 PRO 81 81 81 PRO PRO P . n A 1 82 MET 82 82 82 MET MET P . n A 1 83 ARG 83 83 83 ARG ARG P . n A 1 84 ILE 84 84 84 ILE ILE P . n A 1 85 GLN 85 85 85 GLN GLN P . n A 1 86 TYR 86 86 86 TYR TYR P . n A 1 87 ALA 87 87 87 ALA ALA P . n A 1 88 LYS 88 88 88 LYS LYS P . n A 1 89 THR 89 89 89 THR THR P . n A 1 90 ASP 90 90 90 ASP ASP P . n A 1 91 SER 91 91 91 SER SER P . n A 1 92 ASP 92 92 92 ASP ASP P . n A 1 93 ILE 93 93 93 ILE ILE P . n A 1 94 ILE 94 94 ? ? ? P . n A 1 95 ALA 95 95 ? ? ? P . n A 1 96 LYS 96 96 ? ? ? P . n A 1 97 MET 97 97 ? ? ? P . n A 1 98 LYS 98 98 ? ? ? P . n B 2 1 GTP 1 8 8 GTP GTP R . n B 2 2 G 2 9 9 G G R . n B 2 3 U 3 10 10 U U R . n B 2 4 C 4 11 11 C C R . n B 2 5 A 5 12 12 A A R . n B 2 6 C 6 13 13 C C R . n B 2 7 G 7 14 14 G G R . n B 2 8 C 8 15 15 C C R . n B 2 9 A 9 16 16 A A R . n B 2 10 C 10 17 17 C C R . n B 2 11 A 11 18 18 A A R . n B 2 12 G 12 19 19 G G R . n B 2 13 G 13 20 20 G G R . n B 2 14 G 14 21 21 G G R . n B 2 15 C 15 22 22 C C R . n B 2 16 A 16 23 23 A A R . n B 2 17 A 17 24 24 A A R . n B 2 18 A 18 25 25 A A R . n B 2 19 C 19 26 26 C C R . n B 2 20 C 20 27 27 C C R . n B 2 21 A 21 28 28 A A R . n B 2 22 U 22 29 29 U U R . n B 2 23 U 23 30 30 U U R . n B 2 24 C 24 31 31 C C R . n B 2 25 G 25 32 32 G G R . n B 2 26 A 26 33 33 A A R . n B 2 27 A 27 34 34 A A R . n B 2 28 A 28 35 35 A A R . n B 2 29 G 29 36 36 G G R . n B 2 30 A 30 37 37 A A R . n B 2 31 G 31 38 38 G G R . n B 2 32 U 32 39 39 U U R . n B 2 33 G 33 40 40 G G R . n B 2 34 G 34 41 41 G G R . n B 2 35 G 35 42 42 G G R . n B 2 36 A 36 43 43 A A R . n B 2 37 C 37 44 44 C C R . n B 2 38 G 38 45 45 G G R . n B 2 39 C 39 46 46 C C R . n B 2 40 A 40 47 47 A A R . n B 2 41 A 41 48 48 A A R . n B 2 42 A 42 49 49 A A R . n B 2 43 G 43 50 50 G G R . n B 2 44 C 44 51 51 C C R . n B 2 45 C 45 52 52 C C R . n B 2 46 U 46 53 53 U U R . n B 2 47 C 47 54 54 C C R . n B 2 48 C 48 55 55 C C R . n B 2 49 G 49 56 56 G G R . n B 2 50 G 50 57 57 G G R . n B 2 51 C 51 58 58 C C R . n B 2 52 C 52 59 59 C C R . n B 2 53 U 53 60 60 U U R . n B 2 54 A 54 61 61 A A R . n B 2 55 A 55 62 62 A A R . n B 2 56 A 56 63 63 A A R . n B 2 57 C 57 64 64 C C R . n B 2 58 C 58 65 65 C C R . n B 2 59 A 59 660 660 A A R . n B 2 60 U 60 661 661 U U R . n B 2 61 U 61 662 662 U U R . n B 2 62 G 62 663 663 G G R . n B 2 63 C 63 664 664 C C R . n B 2 64 A 64 665 665 A A R . n B 2 65 C 65 666 666 C C R . n B 2 66 U 66 667 667 U U R . n B 2 67 C 67 668 668 C C R . n B 2 68 C 68 669 669 C C R . n B 2 69 G 69 75 75 G G R . n B 2 70 G 70 76 76 G G R . n B 2 71 U 71 77 77 U U R . n B 2 72 A 72 78 78 A A R . n B 2 73 G 73 79 79 G G R . n B 2 74 G 74 80 80 G G R . n B 2 75 U 75 81 81 U U R . n B 2 76 A 76 82 82 A A R . n B 2 77 G 77 83 83 G G R . n B 2 78 C 78 84 84 C C R . n B 2 79 G 79 85 85 G G R . n B 2 80 G 80 86 86 G G R . n B 2 81 G 81 87 87 G G R . n B 2 82 G 82 88 88 G G R . n B 2 83 U 83 89 89 U U R . n B 2 84 U 84 90 90 U U R . n B 2 85 A 85 91 91 A A R . n B 2 86 U 86 92 92 U U R . n B 2 87 C 87 93 93 C C R . n B 2 88 G 88 94 94 G G R . n B 2 89 A 89 95 95 A A R . n B 2 90 U 90 96 96 U U R . n B 2 91 G 91 97 97 G G R . n B 2 92 G 92 98 98 G G R . n C 3 1 G 1 1 1 G G B . n C 3 2 A 2 2 2 A A B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 MG 1 99 1 MG MO6 P . E 5 HOH 1 100 2 HOH HOH P . E 5 HOH 2 101 1 HOH MO6 P . E 5 HOH 3 102 1 HOH MO6 P . E 5 HOH 4 103 1 HOH MO6 P . E 5 HOH 5 104 1 HOH MO6 P . E 5 HOH 6 105 1 HOH MO6 P . F 5 HOH 1 1 1 HOH HOH R . F 5 HOH 2 3 3 HOH HOH R . F 5 HOH 3 4 4 HOH HOH R . F 5 HOH 4 5 5 HOH HOH R . G 5 HOH 1 6 6 HOH HOH B . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id B _pdbx_struct_mod_residue.label_comp_id GTP _pdbx_struct_mod_residue.label_seq_id 1 _pdbx_struct_mod_residue.auth_asym_id R _pdbx_struct_mod_residue.auth_comp_id GTP _pdbx_struct_mod_residue.auth_seq_id 8 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id G _pdbx_struct_mod_residue.details "GUANOSINE-5'-TRIPHOSPHATE" # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? P HOH 101 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 102 ? 1_555 178.5 ? 2 O ? E HOH . ? P HOH 101 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 103 ? 1_555 85.8 ? 3 O ? E HOH . ? P HOH 102 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 103 ? 1_555 93.6 ? 4 O ? E HOH . ? P HOH 101 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 104 ? 1_555 94.5 ? 5 O ? E HOH . ? P HOH 102 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 104 ? 1_555 86.1 ? 6 O ? E HOH . ? P HOH 103 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 104 ? 1_555 179.2 ? 7 O ? E HOH . ? P HOH 101 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 105 ? 1_555 92.0 ? 8 O ? E HOH . ? P HOH 102 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 105 ? 1_555 86.7 ? 9 O ? E HOH . ? P HOH 103 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 105 ? 1_555 90.0 ? 10 O ? E HOH . ? P HOH 104 ? 1_555 MG ? D MG . ? P MG 99 ? 1_555 O ? E HOH . ? P HOH 105 ? 1_555 90.8 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-01-04 2 'Structure model' 1 1 2012-10-17 3 'Structure model' 1 2 2023-09-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_ref_seq_dif 8 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.value' 6 3 'Structure model' '_struct_conn.pdbx_dist_value' 7 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 9 3 'Structure model' '_struct_ref_seq_dif.details' 10 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 11 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 12 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 15.1230 17.8231 0.3072 0.0723 0.1964 0.2301 0.0173 -0.0909 -0.0525 7.6046 15.2217 2.6864 -0.0875 2.9003 -1.5132 -0.1095 0.1453 -0.0766 0.3003 0.1844 0.1064 -0.2409 0.2391 -0.0749 'X-RAY DIFFRACTION' 2 ? refined 12.7649 -2.9565 38.4103 0.4116 0.2264 0.2872 0.0378 0.1059 0.0101 1.8423 1.4231 1.8337 0.6715 -0.1596 -0.2354 0.1521 -0.0140 -0.0170 0.1865 -0.0676 0.2589 -0.0760 -0.3832 -0.0845 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 P 7 ? ? P 93 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 R 8 ? ? R 98 ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 PHASER phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 OD1 P ASP 79 ? ? 1_555 O P HOH 103 ? ? 2_645 2.10 2 1 OD1 P ASP 79 ? ? 1_555 O P HOH 102 ? ? 2_645 2.11 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" R A 48 ? ? "C1'" R A 48 ? ? N9 R A 48 ? ? 113.52 108.50 5.02 0.70 N 2 1 "C4'" R U 96 ? ? "C3'" R U 96 ? ? "C2'" R U 96 ? ? 96.47 102.60 -6.13 1.00 N 3 1 "C3'" R U 96 ? ? "C2'" R U 96 ? ? "C1'" R U 96 ? ? 96.83 101.30 -4.47 0.70 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ASP P 79 ? ? 78.02 -39.11 2 1 SER P 91 ? ? 32.23 44.01 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 P MET 1 ? A MET 1 2 1 Y 1 P ALA 2 ? A ALA 2 3 1 Y 1 P VAL 3 ? A VAL 3 4 1 Y 1 P PRO 4 ? A PRO 4 5 1 Y 1 P GLU 5 ? A GLU 5 6 1 Y 1 P THR 6 ? A THR 6 7 1 Y 1 P ILE 94 ? A ILE 94 8 1 Y 1 P ALA 95 ? A ALA 95 9 1 Y 1 P LYS 96 ? A LYS 96 10 1 Y 1 P MET 97 ? A MET 97 11 1 Y 1 P LYS 98 ? A LYS 98 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 ALA N N N N 38 ALA CA C N S 39 ALA C C N N 40 ALA O O N N 41 ALA CB C N N 42 ALA OXT O N N 43 ALA H H N N 44 ALA H2 H N N 45 ALA HA H N N 46 ALA HB1 H N N 47 ALA HB2 H N N 48 ALA HB3 H N N 49 ALA HXT H N N 50 ARG N N N N 51 ARG CA C N S 52 ARG C C N N 53 ARG O O N N 54 ARG CB C N N 55 ARG CG C N N 56 ARG CD C N N 57 ARG NE N N N 58 ARG CZ C N N 59 ARG NH1 N N N 60 ARG NH2 N N N 61 ARG OXT O N N 62 ARG H H N N 63 ARG H2 H N N 64 ARG HA H N N 65 ARG HB2 H N N 66 ARG HB3 H N N 67 ARG HG2 H N N 68 ARG HG3 H N N 69 ARG HD2 H N N 70 ARG HD3 H N N 71 ARG HE H N N 72 ARG HH11 H N N 73 ARG HH12 H N N 74 ARG HH21 H N N 75 ARG HH22 H N N 76 ARG HXT H N N 77 ASN N N N N 78 ASN CA C N S 79 ASN C C N N 80 ASN O O N N 81 ASN CB C N N 82 ASN CG C N N 83 ASN OD1 O N N 84 ASN ND2 N N N 85 ASN OXT O N N 86 ASN H H N N 87 ASN H2 H N N 88 ASN HA H N N 89 ASN HB2 H N N 90 ASN HB3 H N N 91 ASN HD21 H N N 92 ASN HD22 H N N 93 ASN HXT H N N 94 ASP N N N N 95 ASP CA C N S 96 ASP C C N N 97 ASP O O N N 98 ASP CB C N N 99 ASP CG C N N 100 ASP OD1 O N N 101 ASP OD2 O N N 102 ASP OXT O N N 103 ASP H H N N 104 ASP H2 H N N 105 ASP HA H N N 106 ASP HB2 H N N 107 ASP HB3 H N N 108 ASP HD2 H N N 109 ASP HXT H N N 110 C OP3 O N N 111 C P P N N 112 C OP1 O N N 113 C OP2 O N N 114 C "O5'" O N N 115 C "C5'" C N N 116 C "C4'" C N R 117 C "O4'" O N N 118 C "C3'" C N S 119 C "O3'" O N N 120 C "C2'" C N R 121 C "O2'" O N N 122 C "C1'" C N R 123 C N1 N N N 124 C C2 C N N 125 C O2 O N N 126 C N3 N N N 127 C C4 C N N 128 C N4 N N N 129 C C5 C N N 130 C C6 C N N 131 C HOP3 H N N 132 C HOP2 H N N 133 C "H5'" H N N 134 C "H5''" H N N 135 C "H4'" H N N 136 C "H3'" H N N 137 C "HO3'" H N N 138 C "H2'" H N N 139 C "HO2'" H N N 140 C "H1'" H N N 141 C H41 H N N 142 C H42 H N N 143 C H5 H N N 144 C H6 H N N 145 G OP3 O N N 146 G P P N N 147 G OP1 O N N 148 G OP2 O N N 149 G "O5'" O N N 150 G "C5'" C N N 151 G "C4'" C N R 152 G "O4'" O N N 153 G "C3'" C N S 154 G "O3'" O N N 155 G "C2'" C N R 156 G "O2'" O N N 157 G "C1'" C N R 158 G N9 N Y N 159 G C8 C Y N 160 G N7 N Y N 161 G C5 C Y N 162 G C6 C N N 163 G O6 O N N 164 G N1 N N N 165 G C2 C N N 166 G N2 N N N 167 G N3 N N N 168 G C4 C Y N 169 G HOP3 H N N 170 G HOP2 H N N 171 G "H5'" H N N 172 G "H5''" H N N 173 G "H4'" H N N 174 G "H3'" H N N 175 G "HO3'" H N N 176 G "H2'" H N N 177 G "HO2'" H N N 178 G "H1'" H N N 179 G H8 H N N 180 G H1 H N N 181 G H21 H N N 182 G H22 H N N 183 GLN N N N N 184 GLN CA C N S 185 GLN C C N N 186 GLN O O N N 187 GLN CB C N N 188 GLN CG C N N 189 GLN CD C N N 190 GLN OE1 O N N 191 GLN NE2 N N N 192 GLN OXT O N N 193 GLN H H N N 194 GLN H2 H N N 195 GLN HA H N N 196 GLN HB2 H N N 197 GLN HB3 H N N 198 GLN HG2 H N N 199 GLN HG3 H N N 200 GLN HE21 H N N 201 GLN HE22 H N N 202 GLN HXT H N N 203 GLU N N N N 204 GLU CA C N S 205 GLU C C N N 206 GLU O O N N 207 GLU CB C N N 208 GLU CG C N N 209 GLU CD C N N 210 GLU OE1 O N N 211 GLU OE2 O N N 212 GLU OXT O N N 213 GLU H H N N 214 GLU H2 H N N 215 GLU HA H N N 216 GLU HB2 H N N 217 GLU HB3 H N N 218 GLU HG2 H N N 219 GLU HG3 H N N 220 GLU HE2 H N N 221 GLU HXT H N N 222 GLY N N N N 223 GLY CA C N N 224 GLY C C N N 225 GLY O O N N 226 GLY OXT O N N 227 GLY H H N N 228 GLY H2 H N N 229 GLY HA2 H N N 230 GLY HA3 H N N 231 GLY HXT H N N 232 GTP PG P N N 233 GTP O1G O N N 234 GTP O2G O N N 235 GTP O3G O N N 236 GTP O3B O N N 237 GTP PB P N N 238 GTP O1B O N N 239 GTP O2B O N N 240 GTP O3A O N N 241 GTP PA P N N 242 GTP O1A O N N 243 GTP O2A O N N 244 GTP "O5'" O N N 245 GTP "C5'" C N N 246 GTP "C4'" C N R 247 GTP "O4'" O N N 248 GTP "C3'" C N S 249 GTP "O3'" O N N 250 GTP "C2'" C N R 251 GTP "O2'" O N N 252 GTP "C1'" C N R 253 GTP N9 N Y N 254 GTP C8 C Y N 255 GTP N7 N Y N 256 GTP C5 C Y N 257 GTP C6 C N N 258 GTP O6 O N N 259 GTP N1 N N N 260 GTP C2 C N N 261 GTP N2 N N N 262 GTP N3 N N N 263 GTP C4 C Y N 264 GTP HOG2 H N N 265 GTP HOG3 H N N 266 GTP HOB2 H N N 267 GTP HOA2 H N N 268 GTP "H5'" H N N 269 GTP "H5''" H N N 270 GTP "H4'" H N N 271 GTP "H3'" H N N 272 GTP "HO3'" H N N 273 GTP "H2'" H N N 274 GTP "HO2'" H N N 275 GTP "H1'" H N N 276 GTP H8 H N N 277 GTP HN1 H N N 278 GTP HN21 H N N 279 GTP HN22 H N N 280 HIS N N N N 281 HIS CA C N S 282 HIS C C N N 283 HIS O O N N 284 HIS CB C N N 285 HIS CG C Y N 286 HIS ND1 N Y N 287 HIS CD2 C Y N 288 HIS CE1 C Y N 289 HIS NE2 N Y N 290 HIS OXT O N N 291 HIS H H N N 292 HIS H2 H N N 293 HIS HA H N N 294 HIS HB2 H N N 295 HIS HB3 H N N 296 HIS HD1 H N N 297 HIS HD2 H N N 298 HIS HE1 H N N 299 HIS HE2 H N N 300 HIS HXT H N N 301 HOH O O N N 302 HOH H1 H N N 303 HOH H2 H N N 304 ILE N N N N 305 ILE CA C N S 306 ILE C C N N 307 ILE O O N N 308 ILE CB C N S 309 ILE CG1 C N N 310 ILE CG2 C N N 311 ILE CD1 C N N 312 ILE OXT O N N 313 ILE H H N N 314 ILE H2 H N N 315 ILE HA H N N 316 ILE HB H N N 317 ILE HG12 H N N 318 ILE HG13 H N N 319 ILE HG21 H N N 320 ILE HG22 H N N 321 ILE HG23 H N N 322 ILE HD11 H N N 323 ILE HD12 H N N 324 ILE HD13 H N N 325 ILE HXT H N N 326 LEU N N N N 327 LEU CA C N S 328 LEU C C N N 329 LEU O O N N 330 LEU CB C N N 331 LEU CG C N N 332 LEU CD1 C N N 333 LEU CD2 C N N 334 LEU OXT O N N 335 LEU H H N N 336 LEU H2 H N N 337 LEU HA H N N 338 LEU HB2 H N N 339 LEU HB3 H N N 340 LEU HG H N N 341 LEU HD11 H N N 342 LEU HD12 H N N 343 LEU HD13 H N N 344 LEU HD21 H N N 345 LEU HD22 H N N 346 LEU HD23 H N N 347 LEU HXT H N N 348 LYS N N N N 349 LYS CA C N S 350 LYS C C N N 351 LYS O O N N 352 LYS CB C N N 353 LYS CG C N N 354 LYS CD C N N 355 LYS CE C N N 356 LYS NZ N N N 357 LYS OXT O N N 358 LYS H H N N 359 LYS H2 H N N 360 LYS HA H N N 361 LYS HB2 H N N 362 LYS HB3 H N N 363 LYS HG2 H N N 364 LYS HG3 H N N 365 LYS HD2 H N N 366 LYS HD3 H N N 367 LYS HE2 H N N 368 LYS HE3 H N N 369 LYS HZ1 H N N 370 LYS HZ2 H N N 371 LYS HZ3 H N N 372 LYS HXT H N N 373 MET N N N N 374 MET CA C N S 375 MET C C N N 376 MET O O N N 377 MET CB C N N 378 MET CG C N N 379 MET SD S N N 380 MET CE C N N 381 MET OXT O N N 382 MET H H N N 383 MET H2 H N N 384 MET HA H N N 385 MET HB2 H N N 386 MET HB3 H N N 387 MET HG2 H N N 388 MET HG3 H N N 389 MET HE1 H N N 390 MET HE2 H N N 391 MET HE3 H N N 392 MET HXT H N N 393 MG MG MG N N 394 PHE N N N N 395 PHE CA C N S 396 PHE C C N N 397 PHE O O N N 398 PHE CB C N N 399 PHE CG C Y N 400 PHE CD1 C Y N 401 PHE CD2 C Y N 402 PHE CE1 C Y N 403 PHE CE2 C Y N 404 PHE CZ C Y N 405 PHE OXT O N N 406 PHE H H N N 407 PHE H2 H N N 408 PHE HA H N N 409 PHE HB2 H N N 410 PHE HB3 H N N 411 PHE HD1 H N N 412 PHE HD2 H N N 413 PHE HE1 H N N 414 PHE HE2 H N N 415 PHE HZ H N N 416 PHE HXT H N N 417 PRO N N N N 418 PRO CA C N S 419 PRO C C N N 420 PRO O O N N 421 PRO CB C N N 422 PRO CG C N N 423 PRO CD C N N 424 PRO OXT O N N 425 PRO H H N N 426 PRO HA H N N 427 PRO HB2 H N N 428 PRO HB3 H N N 429 PRO HG2 H N N 430 PRO HG3 H N N 431 PRO HD2 H N N 432 PRO HD3 H N N 433 PRO HXT H N N 434 SER N N N N 435 SER CA C N S 436 SER C C N N 437 SER O O N N 438 SER CB C N N 439 SER OG O N N 440 SER OXT O N N 441 SER H H N N 442 SER H2 H N N 443 SER HA H N N 444 SER HB2 H N N 445 SER HB3 H N N 446 SER HG H N N 447 SER HXT H N N 448 THR N N N N 449 THR CA C N S 450 THR C C N N 451 THR O O N N 452 THR CB C N R 453 THR OG1 O N N 454 THR CG2 C N N 455 THR OXT O N N 456 THR H H N N 457 THR H2 H N N 458 THR HA H N N 459 THR HB H N N 460 THR HG1 H N N 461 THR HG21 H N N 462 THR HG22 H N N 463 THR HG23 H N N 464 THR HXT H N N 465 TYR N N N N 466 TYR CA C N S 467 TYR C C N N 468 TYR O O N N 469 TYR CB C N N 470 TYR CG C Y N 471 TYR CD1 C Y N 472 TYR CD2 C Y N 473 TYR CE1 C Y N 474 TYR CE2 C Y N 475 TYR CZ C Y N 476 TYR OH O N N 477 TYR OXT O N N 478 TYR H H N N 479 TYR H2 H N N 480 TYR HA H N N 481 TYR HB2 H N N 482 TYR HB3 H N N 483 TYR HD1 H N N 484 TYR HD2 H N N 485 TYR HE1 H N N 486 TYR HE2 H N N 487 TYR HH H N N 488 TYR HXT H N N 489 U OP3 O N N 490 U P P N N 491 U OP1 O N N 492 U OP2 O N N 493 U "O5'" O N N 494 U "C5'" C N N 495 U "C4'" C N R 496 U "O4'" O N N 497 U "C3'" C N S 498 U "O3'" O N N 499 U "C2'" C N R 500 U "O2'" O N N 501 U "C1'" C N R 502 U N1 N N N 503 U C2 C N N 504 U O2 O N N 505 U N3 N N N 506 U C4 C N N 507 U O4 O N N 508 U C5 C N N 509 U C6 C N N 510 U HOP3 H N N 511 U HOP2 H N N 512 U "H5'" H N N 513 U "H5''" H N N 514 U "H4'" H N N 515 U "H3'" H N N 516 U "HO3'" H N N 517 U "H2'" H N N 518 U "HO2'" H N N 519 U "H1'" H N N 520 U H3 H N N 521 U H5 H N N 522 U H6 H N N 523 VAL N N N N 524 VAL CA C N S 525 VAL C C N N 526 VAL O O N N 527 VAL CB C N N 528 VAL CG1 C N N 529 VAL CG2 C N N 530 VAL OXT O N N 531 VAL H H N N 532 VAL H2 H N N 533 VAL HA H N N 534 VAL HB H N N 535 VAL HG11 H N N 536 VAL HG12 H N N 537 VAL HG13 H N N 538 VAL HG21 H N N 539 VAL HG22 H N N 540 VAL HG23 H N N 541 VAL HXT H N N 542 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 ALA N CA sing N N 40 ALA N H sing N N 41 ALA N H2 sing N N 42 ALA CA C sing N N 43 ALA CA CB sing N N 44 ALA CA HA sing N N 45 ALA C O doub N N 46 ALA C OXT sing N N 47 ALA CB HB1 sing N N 48 ALA CB HB2 sing N N 49 ALA CB HB3 sing N N 50 ALA OXT HXT sing N N 51 ARG N CA sing N N 52 ARG N H sing N N 53 ARG N H2 sing N N 54 ARG CA C sing N N 55 ARG CA CB sing N N 56 ARG CA HA sing N N 57 ARG C O doub N N 58 ARG C OXT sing N N 59 ARG CB CG sing N N 60 ARG CB HB2 sing N N 61 ARG CB HB3 sing N N 62 ARG CG CD sing N N 63 ARG CG HG2 sing N N 64 ARG CG HG3 sing N N 65 ARG CD NE sing N N 66 ARG CD HD2 sing N N 67 ARG CD HD3 sing N N 68 ARG NE CZ sing N N 69 ARG NE HE sing N N 70 ARG CZ NH1 sing N N 71 ARG CZ NH2 doub N N 72 ARG NH1 HH11 sing N N 73 ARG NH1 HH12 sing N N 74 ARG NH2 HH21 sing N N 75 ARG NH2 HH22 sing N N 76 ARG OXT HXT sing N N 77 ASN N CA sing N N 78 ASN N H sing N N 79 ASN N H2 sing N N 80 ASN CA C sing N N 81 ASN CA CB sing N N 82 ASN CA HA sing N N 83 ASN C O doub N N 84 ASN C OXT sing N N 85 ASN CB CG sing N N 86 ASN CB HB2 sing N N 87 ASN CB HB3 sing N N 88 ASN CG OD1 doub N N 89 ASN CG ND2 sing N N 90 ASN ND2 HD21 sing N N 91 ASN ND2 HD22 sing N N 92 ASN OXT HXT sing N N 93 ASP N CA sing N N 94 ASP N H sing N N 95 ASP N H2 sing N N 96 ASP CA C sing N N 97 ASP CA CB sing N N 98 ASP CA HA sing N N 99 ASP C O doub N N 100 ASP C OXT sing N N 101 ASP CB CG sing N N 102 ASP CB HB2 sing N N 103 ASP CB HB3 sing N N 104 ASP CG OD1 doub N N 105 ASP CG OD2 sing N N 106 ASP OD2 HD2 sing N N 107 ASP OXT HXT sing N N 108 C OP3 P sing N N 109 C OP3 HOP3 sing N N 110 C P OP1 doub N N 111 C P OP2 sing N N 112 C P "O5'" sing N N 113 C OP2 HOP2 sing N N 114 C "O5'" "C5'" sing N N 115 C "C5'" "C4'" sing N N 116 C "C5'" "H5'" sing N N 117 C "C5'" "H5''" sing N N 118 C "C4'" "O4'" sing N N 119 C "C4'" "C3'" sing N N 120 C "C4'" "H4'" sing N N 121 C "O4'" "C1'" sing N N 122 C "C3'" "O3'" sing N N 123 C "C3'" "C2'" sing N N 124 C "C3'" "H3'" sing N N 125 C "O3'" "HO3'" sing N N 126 C "C2'" "O2'" sing N N 127 C "C2'" "C1'" sing N N 128 C "C2'" "H2'" sing N N 129 C "O2'" "HO2'" sing N N 130 C "C1'" N1 sing N N 131 C "C1'" "H1'" sing N N 132 C N1 C2 sing N N 133 C N1 C6 sing N N 134 C C2 O2 doub N N 135 C C2 N3 sing N N 136 C N3 C4 doub N N 137 C C4 N4 sing N N 138 C C4 C5 sing N N 139 C N4 H41 sing N N 140 C N4 H42 sing N N 141 C C5 C6 doub N N 142 C C5 H5 sing N N 143 C C6 H6 sing N N 144 G OP3 P sing N N 145 G OP3 HOP3 sing N N 146 G P OP1 doub N N 147 G P OP2 sing N N 148 G P "O5'" sing N N 149 G OP2 HOP2 sing N N 150 G "O5'" "C5'" sing N N 151 G "C5'" "C4'" sing N N 152 G "C5'" "H5'" sing N N 153 G "C5'" "H5''" sing N N 154 G "C4'" "O4'" sing N N 155 G "C4'" "C3'" sing N N 156 G "C4'" "H4'" sing N N 157 G "O4'" "C1'" sing N N 158 G "C3'" "O3'" sing N N 159 G "C3'" "C2'" sing N N 160 G "C3'" "H3'" sing N N 161 G "O3'" "HO3'" sing N N 162 G "C2'" "O2'" sing N N 163 G "C2'" "C1'" sing N N 164 G "C2'" "H2'" sing N N 165 G "O2'" "HO2'" sing N N 166 G "C1'" N9 sing N N 167 G "C1'" "H1'" sing N N 168 G N9 C8 sing Y N 169 G N9 C4 sing Y N 170 G C8 N7 doub Y N 171 G C8 H8 sing N N 172 G N7 C5 sing Y N 173 G C5 C6 sing N N 174 G C5 C4 doub Y N 175 G C6 O6 doub N N 176 G C6 N1 sing N N 177 G N1 C2 sing N N 178 G N1 H1 sing N N 179 G C2 N2 sing N N 180 G C2 N3 doub N N 181 G N2 H21 sing N N 182 G N2 H22 sing N N 183 G N3 C4 sing N N 184 GLN N CA sing N N 185 GLN N H sing N N 186 GLN N H2 sing N N 187 GLN CA C sing N N 188 GLN CA CB sing N N 189 GLN CA HA sing N N 190 GLN C O doub N N 191 GLN C OXT sing N N 192 GLN CB CG sing N N 193 GLN CB HB2 sing N N 194 GLN CB HB3 sing N N 195 GLN CG CD sing N N 196 GLN CG HG2 sing N N 197 GLN CG HG3 sing N N 198 GLN CD OE1 doub N N 199 GLN CD NE2 sing N N 200 GLN NE2 HE21 sing N N 201 GLN NE2 HE22 sing N N 202 GLN OXT HXT sing N N 203 GLU N CA sing N N 204 GLU N H sing N N 205 GLU N H2 sing N N 206 GLU CA C sing N N 207 GLU CA CB sing N N 208 GLU CA HA sing N N 209 GLU C O doub N N 210 GLU C OXT sing N N 211 GLU CB CG sing N N 212 GLU CB HB2 sing N N 213 GLU CB HB3 sing N N 214 GLU CG CD sing N N 215 GLU CG HG2 sing N N 216 GLU CG HG3 sing N N 217 GLU CD OE1 doub N N 218 GLU CD OE2 sing N N 219 GLU OE2 HE2 sing N N 220 GLU OXT HXT sing N N 221 GLY N CA sing N N 222 GLY N H sing N N 223 GLY N H2 sing N N 224 GLY CA C sing N N 225 GLY CA HA2 sing N N 226 GLY CA HA3 sing N N 227 GLY C O doub N N 228 GLY C OXT sing N N 229 GLY OXT HXT sing N N 230 GTP PG O1G doub N N 231 GTP PG O2G sing N N 232 GTP PG O3G sing N N 233 GTP PG O3B sing N N 234 GTP O2G HOG2 sing N N 235 GTP O3G HOG3 sing N N 236 GTP O3B PB sing N N 237 GTP PB O1B doub N N 238 GTP PB O2B sing N N 239 GTP PB O3A sing N N 240 GTP O2B HOB2 sing N N 241 GTP O3A PA sing N N 242 GTP PA O1A doub N N 243 GTP PA O2A sing N N 244 GTP PA "O5'" sing N N 245 GTP O2A HOA2 sing N N 246 GTP "O5'" "C5'" sing N N 247 GTP "C5'" "C4'" sing N N 248 GTP "C5'" "H5'" sing N N 249 GTP "C5'" "H5''" sing N N 250 GTP "C4'" "O4'" sing N N 251 GTP "C4'" "C3'" sing N N 252 GTP "C4'" "H4'" sing N N 253 GTP "O4'" "C1'" sing N N 254 GTP "C3'" "O3'" sing N N 255 GTP "C3'" "C2'" sing N N 256 GTP "C3'" "H3'" sing N N 257 GTP "O3'" "HO3'" sing N N 258 GTP "C2'" "O2'" sing N N 259 GTP "C2'" "C1'" sing N N 260 GTP "C2'" "H2'" sing N N 261 GTP "O2'" "HO2'" sing N N 262 GTP "C1'" N9 sing N N 263 GTP "C1'" "H1'" sing N N 264 GTP N9 C8 sing Y N 265 GTP N9 C4 sing Y N 266 GTP C8 N7 doub Y N 267 GTP C8 H8 sing N N 268 GTP N7 C5 sing Y N 269 GTP C5 C6 sing N N 270 GTP C5 C4 doub Y N 271 GTP C6 O6 doub N N 272 GTP C6 N1 sing N N 273 GTP N1 C2 sing N N 274 GTP N1 HN1 sing N N 275 GTP C2 N2 sing N N 276 GTP C2 N3 doub N N 277 GTP N2 HN21 sing N N 278 GTP N2 HN22 sing N N 279 GTP N3 C4 sing N N 280 HIS N CA sing N N 281 HIS N H sing N N 282 HIS N H2 sing N N 283 HIS CA C sing N N 284 HIS CA CB sing N N 285 HIS CA HA sing N N 286 HIS C O doub N N 287 HIS C OXT sing N N 288 HIS CB CG sing N N 289 HIS CB HB2 sing N N 290 HIS CB HB3 sing N N 291 HIS CG ND1 sing Y N 292 HIS CG CD2 doub Y N 293 HIS ND1 CE1 doub Y N 294 HIS ND1 HD1 sing N N 295 HIS CD2 NE2 sing Y N 296 HIS CD2 HD2 sing N N 297 HIS CE1 NE2 sing Y N 298 HIS CE1 HE1 sing N N 299 HIS NE2 HE2 sing N N 300 HIS OXT HXT sing N N 301 HOH O H1 sing N N 302 HOH O H2 sing N N 303 ILE N CA sing N N 304 ILE N H sing N N 305 ILE N H2 sing N N 306 ILE CA C sing N N 307 ILE CA CB sing N N 308 ILE CA HA sing N N 309 ILE C O doub N N 310 ILE C OXT sing N N 311 ILE CB CG1 sing N N 312 ILE CB CG2 sing N N 313 ILE CB HB sing N N 314 ILE CG1 CD1 sing N N 315 ILE CG1 HG12 sing N N 316 ILE CG1 HG13 sing N N 317 ILE CG2 HG21 sing N N 318 ILE CG2 HG22 sing N N 319 ILE CG2 HG23 sing N N 320 ILE CD1 HD11 sing N N 321 ILE CD1 HD12 sing N N 322 ILE CD1 HD13 sing N N 323 ILE OXT HXT sing N N 324 LEU N CA sing N N 325 LEU N H sing N N 326 LEU N H2 sing N N 327 LEU CA C sing N N 328 LEU CA CB sing N N 329 LEU CA HA sing N N 330 LEU C O doub N N 331 LEU C OXT sing N N 332 LEU CB CG sing N N 333 LEU CB HB2 sing N N 334 LEU CB HB3 sing N N 335 LEU CG CD1 sing N N 336 LEU CG CD2 sing N N 337 LEU CG HG sing N N 338 LEU CD1 HD11 sing N N 339 LEU CD1 HD12 sing N N 340 LEU CD1 HD13 sing N N 341 LEU CD2 HD21 sing N N 342 LEU CD2 HD22 sing N N 343 LEU CD2 HD23 sing N N 344 LEU OXT HXT sing N N 345 LYS N CA sing N N 346 LYS N H sing N N 347 LYS N H2 sing N N 348 LYS CA C sing N N 349 LYS CA CB sing N N 350 LYS CA HA sing N N 351 LYS C O doub N N 352 LYS C OXT sing N N 353 LYS CB CG sing N N 354 LYS CB HB2 sing N N 355 LYS CB HB3 sing N N 356 LYS CG CD sing N N 357 LYS CG HG2 sing N N 358 LYS CG HG3 sing N N 359 LYS CD CE sing N N 360 LYS CD HD2 sing N N 361 LYS CD HD3 sing N N 362 LYS CE NZ sing N N 363 LYS CE HE2 sing N N 364 LYS CE HE3 sing N N 365 LYS NZ HZ1 sing N N 366 LYS NZ HZ2 sing N N 367 LYS NZ HZ3 sing N N 368 LYS OXT HXT sing N N 369 MET N CA sing N N 370 MET N H sing N N 371 MET N H2 sing N N 372 MET CA C sing N N 373 MET CA CB sing N N 374 MET CA HA sing N N 375 MET C O doub N N 376 MET C OXT sing N N 377 MET CB CG sing N N 378 MET CB HB2 sing N N 379 MET CB HB3 sing N N 380 MET CG SD sing N N 381 MET CG HG2 sing N N 382 MET CG HG3 sing N N 383 MET SD CE sing N N 384 MET CE HE1 sing N N 385 MET CE HE2 sing N N 386 MET CE HE3 sing N N 387 MET OXT HXT sing N N 388 PHE N CA sing N N 389 PHE N H sing N N 390 PHE N H2 sing N N 391 PHE CA C sing N N 392 PHE CA CB sing N N 393 PHE CA HA sing N N 394 PHE C O doub N N 395 PHE C OXT sing N N 396 PHE CB CG sing N N 397 PHE CB HB2 sing N N 398 PHE CB HB3 sing N N 399 PHE CG CD1 doub Y N 400 PHE CG CD2 sing Y N 401 PHE CD1 CE1 sing Y N 402 PHE CD1 HD1 sing N N 403 PHE CD2 CE2 doub Y N 404 PHE CD2 HD2 sing N N 405 PHE CE1 CZ doub Y N 406 PHE CE1 HE1 sing N N 407 PHE CE2 CZ sing Y N 408 PHE CE2 HE2 sing N N 409 PHE CZ HZ sing N N 410 PHE OXT HXT sing N N 411 PRO N CA sing N N 412 PRO N CD sing N N 413 PRO N H sing N N 414 PRO CA C sing N N 415 PRO CA CB sing N N 416 PRO CA HA sing N N 417 PRO C O doub N N 418 PRO C OXT sing N N 419 PRO CB CG sing N N 420 PRO CB HB2 sing N N 421 PRO CB HB3 sing N N 422 PRO CG CD sing N N 423 PRO CG HG2 sing N N 424 PRO CG HG3 sing N N 425 PRO CD HD2 sing N N 426 PRO CD HD3 sing N N 427 PRO OXT HXT sing N N 428 SER N CA sing N N 429 SER N H sing N N 430 SER N H2 sing N N 431 SER CA C sing N N 432 SER CA CB sing N N 433 SER CA HA sing N N 434 SER C O doub N N 435 SER C OXT sing N N 436 SER CB OG sing N N 437 SER CB HB2 sing N N 438 SER CB HB3 sing N N 439 SER OG HG sing N N 440 SER OXT HXT sing N N 441 THR N CA sing N N 442 THR N H sing N N 443 THR N H2 sing N N 444 THR CA C sing N N 445 THR CA CB sing N N 446 THR CA HA sing N N 447 THR C O doub N N 448 THR C OXT sing N N 449 THR CB OG1 sing N N 450 THR CB CG2 sing N N 451 THR CB HB sing N N 452 THR OG1 HG1 sing N N 453 THR CG2 HG21 sing N N 454 THR CG2 HG22 sing N N 455 THR CG2 HG23 sing N N 456 THR OXT HXT sing N N 457 TYR N CA sing N N 458 TYR N H sing N N 459 TYR N H2 sing N N 460 TYR CA C sing N N 461 TYR CA CB sing N N 462 TYR CA HA sing N N 463 TYR C O doub N N 464 TYR C OXT sing N N 465 TYR CB CG sing N N 466 TYR CB HB2 sing N N 467 TYR CB HB3 sing N N 468 TYR CG CD1 doub Y N 469 TYR CG CD2 sing Y N 470 TYR CD1 CE1 sing Y N 471 TYR CD1 HD1 sing N N 472 TYR CD2 CE2 doub Y N 473 TYR CD2 HD2 sing N N 474 TYR CE1 CZ doub Y N 475 TYR CE1 HE1 sing N N 476 TYR CE2 CZ sing Y N 477 TYR CE2 HE2 sing N N 478 TYR CZ OH sing N N 479 TYR OH HH sing N N 480 TYR OXT HXT sing N N 481 U OP3 P sing N N 482 U OP3 HOP3 sing N N 483 U P OP1 doub N N 484 U P OP2 sing N N 485 U P "O5'" sing N N 486 U OP2 HOP2 sing N N 487 U "O5'" "C5'" sing N N 488 U "C5'" "C4'" sing N N 489 U "C5'" "H5'" sing N N 490 U "C5'" "H5''" sing N N 491 U "C4'" "O4'" sing N N 492 U "C4'" "C3'" sing N N 493 U "C4'" "H4'" sing N N 494 U "O4'" "C1'" sing N N 495 U "C3'" "O3'" sing N N 496 U "C3'" "C2'" sing N N 497 U "C3'" "H3'" sing N N 498 U "O3'" "HO3'" sing N N 499 U "C2'" "O2'" sing N N 500 U "C2'" "C1'" sing N N 501 U "C2'" "H2'" sing N N 502 U "O2'" "HO2'" sing N N 503 U "C1'" N1 sing N N 504 U "C1'" "H1'" sing N N 505 U N1 C2 sing N N 506 U N1 C6 sing N N 507 U C2 O2 doub N N 508 U C2 N3 sing N N 509 U N3 C4 sing N N 510 U N3 H3 sing N N 511 U C4 O4 doub N N 512 U C4 C5 sing N N 513 U C5 C6 doub N N 514 U C5 H5 sing N N 515 U C6 H6 sing N N 516 VAL N CA sing N N 517 VAL N H sing N N 518 VAL N H2 sing N N 519 VAL CA C sing N N 520 VAL CA CB sing N N 521 VAL CA HA sing N N 522 VAL C O doub N N 523 VAL C OXT sing N N 524 VAL CB CG1 sing N N 525 VAL CB CG2 sing N N 526 VAL CB HB sing N N 527 VAL CG1 HG11 sing N N 528 VAL CG1 HG12 sing N N 529 VAL CG1 HG13 sing N N 530 VAL CG2 HG21 sing N N 531 VAL CG2 HG22 sing N N 532 VAL CG2 HG23 sing N N 533 VAL OXT HXT sing N N 534 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3UD4 'double helix' 3UD4 'a-form double helix' 3UD4 'hairpin loop' 3UD4 tetraloop 3UD4 'bulge loop' 3UD4 'mismatched base pair' 3UD4 'triple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 B C 4 1_555 B G 92 1_555 -0.369 0.080 -0.328 12.087 -12.400 6.553 1 R_C11:G98_R R 11 ? R 98 ? 19 1 1 B A 5 1_555 B G 91 1_555 0.402 1.385 -0.691 -8.729 -18.034 0.784 2 R_A12:G97_R R 12 ? R 97 ? 8 1 1 B C 6 1_555 B G 88 1_555 -0.024 -0.116 0.231 -19.998 -14.675 -1.490 3 R_C13:G94_R R 13 ? R 94 ? 19 1 1 B G 7 1_555 B C 87 1_555 -0.441 0.078 0.156 6.417 -6.577 -1.023 4 R_G14:C93_R R 14 ? R 93 ? 19 1 1 C A 2 1_555 B U 86 1_555 -0.409 0.059 -0.111 2.919 -12.780 9.657 5 B_A2:U92_R B 2 ? R 92 ? 20 1 1 B G 12 1_555 B A 40 1_555 -0.528 2.857 0.162 -6.248 8.828 -66.337 6 R_G19:A47_R R 19 ? R 47 ? ? ? 1 B G 13 1_555 C G 1 1_555 5.600 -0.257 -0.116 18.116 -4.678 -114.736 7 R_G20:G1_B R 20 ? B 1 ? 7 4 1 B G 14 1_555 B C 39 1_555 -0.200 0.099 -0.548 -6.375 2.580 4.513 8 R_G21:C46_R R 21 ? R 46 ? 19 1 1 B C 15 1_555 B G 38 1_555 0.294 -0.282 -0.193 5.019 3.289 0.656 9 R_C22:G45_R R 22 ? R 45 ? 19 1 1 B G 77 1_555 B C 37 1_555 -0.593 -0.338 0.449 0.145 -5.742 -1.860 10 R_G83:C44_R R 83 ? R 44 ? 19 1 1 B A 18 1_555 B G 35 1_555 -6.818 -3.767 0.155 2.295 -11.386 2.203 11 R_A25:G42_R R 25 ? R 42 ? 11 9 1 B C 19 1_555 B G 34 1_555 0.014 -0.044 -0.326 6.896 -10.672 -0.128 12 R_C26:G41_R R 26 ? R 41 ? 19 1 1 B C 20 1_555 B G 33 1_555 0.123 -0.107 -0.214 8.046 -8.415 1.296 13 R_C27:G40_R R 27 ? R 40 ? 19 1 1 B A 21 1_555 B U 32 1_555 0.395 -0.196 0.066 4.787 -14.878 1.039 14 R_A28:U39_R R 28 ? R 39 ? 20 1 1 B U 22 1_555 B G 31 1_555 2.283 -0.612 -0.276 4.867 -18.028 1.373 15 R_U29:G38_R R 29 ? R 38 ? 28 1 1 B U 23 1_555 B A 30 1_555 0.143 -0.283 0.266 -7.661 -9.248 -0.879 16 R_U30:A37_R R 30 ? R 37 ? 20 1 1 B C 24 1_555 B G 29 1_555 -0.046 -0.216 -0.219 4.107 -4.213 -0.936 17 R_C31:G36_R R 31 ? R 36 ? 19 1 1 B A 41 1_555 B U 84 1_555 -4.386 -2.689 -0.332 12.822 -1.449 -85.369 18 R_A48:U90_R R 48 ? R 90 ? 24 4 1 B G 43 1_555 B U 83 1_555 -2.367 -0.670 0.160 1.912 -13.785 -7.440 19 R_G50:U89_R R 50 ? R 89 ? 28 1 1 B C 44 1_555 B G 82 1_555 -0.082 -0.300 -0.077 5.334 -16.778 -0.865 20 R_C51:G88_R R 51 ? R 88 ? 19 1 1 B C 45 1_555 B G 81 1_555 0.466 0.088 0.482 -7.867 -3.799 3.823 21 R_C52:G87_R R 52 ? R 87 ? 19 1 1 B C 47 1_555 B G 80 1_555 -0.319 -0.168 -0.377 13.655 -10.360 -1.917 22 R_C54:G86_R R 54 ? R 86 ? 19 1 1 B C 48 1_555 B G 79 1_555 0.303 -0.285 -0.156 -2.156 -2.127 -0.526 23 R_C55:G85_R R 55 ? R 85 ? 19 1 1 B G 49 1_555 B C 78 1_555 0.099 -0.149 0.253 5.431 -0.059 -0.202 24 R_G56:C84_R R 56 ? R 84 ? 19 1 1 B G 50 1_555 B U 75 1_555 -2.060 -0.523 0.069 3.751 -5.929 -9.539 25 R_G57:U81_R R 57 ? R 81 ? 28 1 1 B C 51 1_555 B G 74 1_555 -0.093 -0.096 -0.287 18.120 -14.657 -0.224 26 R_C58:G80_R R 58 ? R 80 ? 19 1 1 B C 52 1_555 B G 73 1_555 0.216 -0.032 -0.244 3.664 -9.669 5.348 27 R_C59:G79_R R 59 ? R 79 ? 19 1 1 B U 53 1_555 B A 72 1_555 -0.331 -0.062 0.074 -4.605 -6.688 2.612 28 R_U60:A78_R R 60 ? R 78 ? 20 1 1 B A 56 1_555 B U 71 1_555 -5.460 -0.354 0.513 27.849 -12.354 24.041 29 R_A63:U77_R R 63 ? R 77 ? ? ? 1 B C 57 1_555 B G 70 1_555 0.150 -0.213 -0.724 25.027 -33.101 6.015 30 R_C64:G76_R R 64 ? R 76 ? 19 1 1 B C 58 1_555 B G 69 1_555 0.381 -0.099 0.021 -0.917 -18.700 5.535 31 R_C65:G75_R R 65 ? R 75 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 B C 4 1_555 B G 92 1_555 B A 5 1_555 B G 91 1_555 1.370 -2.380 3.899 2.903 14.857 33.024 -6.043 -1.770 2.721 24.592 -4.805 36.241 1 RR_C11A12:G97G98_RR R 11 ? R 98 ? R 12 ? R 97 ? 1 B A 5 1_555 B G 91 1_555 B C 6 1_555 B G 88 1_555 2.472 -0.516 3.072 4.337 9.157 51.630 -1.156 -2.521 3.129 10.400 -4.926 52.548 2 RR_A12C13:G94G97_RR R 12 ? R 97 ? R 13 ? R 94 ? 1 B C 6 1_555 B G 88 1_555 B G 7 1_555 B C 87 1_555 -0.751 -0.655 2.681 -3.357 21.267 25.467 -3.886 0.881 1.729 40.282 6.358 33.233 3 RR_C13G14:C93G94_RR R 13 ? R 94 ? R 14 ? R 93 ? 1 B G 7 1_555 B C 87 1_555 C A 2 1_555 B U 86 1_555 -0.511 -0.879 3.251 -2.363 5.807 39.694 -1.927 0.480 3.121 8.487 3.454 40.166 4 RB_G14A2:U92C93_RR R 14 ? R 93 ? B 2 ? R 92 ? 1 C A 2 1_555 B U 86 1_555 B G 12 1_555 B A 40 1_555 -3.302 2.288 3.337 -4.758 -3.518 115.626 1.389 1.898 3.377 -2.077 2.810 115.722 5 BR_A2G19:A47U92_RR B 2 ? R 92 ? R 19 ? R 47 ? 1 B G 12 1_555 B A 40 1_555 B G 13 1_555 C G 1 1_555 -0.254 -3.213 2.959 -3.976 2.565 49.025 -4.026 0.042 2.809 3.083 4.779 49.238 6 RR_G19G20:G1A47_BR R 19 ? R 47 ? R 20 ? B 1 ? 1 B G 13 1_555 C G 1 1_555 B G 14 1_555 B C 39 1_555 1.919 -1.785 3.973 2.065 -1.411 -24.936 4.606 5.141 3.700 3.257 4.768 -25.059 7 RR_G20G21:C46G1_RB R 20 ? B 1 ? R 21 ? R 46 ? 1 B G 14 1_555 B C 39 1_555 B C 15 1_555 B G 38 1_555 -0.048 -1.933 3.112 -3.522 -1.516 31.218 -3.293 -0.548 3.186 -2.803 6.513 31.447 8 RR_G21C22:G45C46_RR R 21 ? R 46 ? R 22 ? R 45 ? 1 B C 15 1_555 B G 38 1_555 B G 77 1_555 B C 37 1_555 -5.349 -0.080 3.515 -13.353 -7.824 54.539 0.470 4.701 4.577 -8.352 14.253 56.530 9 RR_C22G83:C44G45_RR R 22 ? R 45 ? R 83 ? R 44 ? 1 B A 18 1_555 B G 35 1_555 B C 19 1_555 B G 34 1_555 -0.436 -0.671 3.426 -3.997 6.483 62.272 -0.949 0.231 3.368 6.244 3.849 62.689 10 RR_A25C26:G41G42_RR R 25 ? R 42 ? R 26 ? R 41 ? 1 B C 19 1_555 B G 34 1_555 B C 20 1_555 B G 33 1_555 -0.068 -1.754 3.233 -1.320 7.675 29.580 -4.732 -0.112 2.703 14.713 2.531 30.566 11 RR_C26C27:G40G41_RR R 26 ? R 41 ? R 27 ? R 40 ? 1 B C 20 1_555 B G 33 1_555 B A 21 1_555 B U 32 1_555 -0.124 -1.377 3.168 -0.799 15.678 36.421 -3.673 0.099 2.401 23.774 1.212 39.554 12 RR_C27A28:U39G40_RR R 27 ? R 40 ? R 28 ? R 39 ? 1 B A 21 1_555 B U 32 1_555 B U 22 1_555 B G 31 1_555 0.100 -1.218 3.303 4.899 8.407 37.185 -2.873 0.443 2.958 12.914 -7.526 38.393 13 RR_A28U29:G38U39_RR R 28 ? R 39 ? R 29 ? R 38 ? 1 B U 22 1_555 B G 31 1_555 B U 23 1_555 B A 30 1_555 0.065 -2.048 3.269 0.616 13.338 25.386 -6.710 -0.014 1.968 28.015 -1.293 28.632 14 RR_U29U30:A37G38_RR R 29 ? R 38 ? R 30 ? R 37 ? 1 B U 23 1_555 B A 30 1_555 B C 24 1_555 B G 29 1_555 0.247 -1.400 2.881 4.933 2.557 31.425 -2.951 0.331 2.767 4.675 -9.019 31.900 15 RR_U30C31:G36A37_RR R 30 ? R 37 ? R 31 ? R 36 ? 1 B A 41 1_555 B U 84 1_555 B G 43 1_555 B U 83 1_555 2.961 -2.199 3.400 -8.983 5.016 66.127 -2.187 -3.029 2.869 4.568 8.181 66.833 16 RR_A48G50:U89U90_RR R 48 ? R 90 ? R 50 ? R 89 ? 1 B G 43 1_555 B U 83 1_555 B C 44 1_555 B G 82 1_555 0.535 -1.395 3.153 0.390 6.459 41.093 -2.604 -0.714 2.915 9.133 -0.551 41.578 17 RR_G50C51:G88U89_RR R 50 ? R 89 ? R 51 ? R 88 ? 1 B C 44 1_555 B G 82 1_555 B C 45 1_555 B G 81 1_555 0.263 -1.926 3.557 -1.294 9.500 37.036 -4.157 -0.567 2.980 14.657 1.996 38.214 18 RR_C51C52:G87G88_RR R 51 ? R 88 ? R 52 ? R 87 ? 1 B C 45 1_555 B G 81 1_555 B C 47 1_555 B G 80 1_555 -3.168 -1.117 2.745 10.051 2.532 49.138 -1.453 4.274 2.045 3.006 -11.932 50.153 19 RR_C52C54:G86G87_RR R 52 ? R 87 ? R 54 ? R 86 ? 1 B C 47 1_555 B G 80 1_555 B C 48 1_555 B G 79 1_555 -0.392 -2.355 3.691 -2.804 9.151 34.763 -5.167 0.218 3.016 14.968 4.586 36.017 20 RR_C54C55:G85G86_RR R 54 ? R 86 ? R 55 ? R 85 ? 1 B C 48 1_555 B G 79 1_555 B G 49 1_555 B C 78 1_555 -0.365 -2.122 2.975 -3.537 5.090 27.037 -5.482 0.028 2.566 10.709 7.441 27.725 21 RR_C55G56:C84G85_RR R 55 ? R 85 ? R 56 ? R 84 ? 1 B G 49 1_555 B C 78 1_555 B G 50 1_555 B U 75 1_555 2.304 -2.114 3.030 2.598 8.502 37.281 -4.162 -3.226 2.651 13.073 -3.995 38.290 22 RR_G56G57:U81C84_RR R 56 ? R 84 ? R 57 ? R 81 ? 1 B G 50 1_555 B U 75 1_555 B C 51 1_555 B G 74 1_555 0.429 -1.417 2.935 -0.710 3.356 41.536 -2.304 -0.668 2.810 4.722 0.999 41.671 23 RR_G57C58:G80U81_RR R 57 ? R 81 ? R 58 ? R 80 ? 1 B C 51 1_555 B G 74 1_555 B C 52 1_555 B G 73 1_555 -0.219 -2.097 3.594 -2.404 9.134 30.026 -5.596 -0.051 2.857 17.106 4.502 31.444 24 RR_C58C59:G79G80_RR R 58 ? R 80 ? R 59 ? R 79 ? 1 B C 52 1_555 B G 73 1_555 B U 53 1_555 B A 72 1_555 -0.195 -1.852 3.556 -1.233 9.998 27.632 -5.785 0.122 2.739 20.106 2.479 29.378 25 RR_C59U60:A78G79_RR R 59 ? R 79 ? R 60 ? R 78 ? 1 B U 53 1_555 B A 72 1_555 B A 56 1_555 B U 71 1_555 -3.344 -2.050 3.691 18.293 18.014 43.694 -3.490 5.027 1.376 22.088 -22.430 50.358 26 RR_U60A63:U77A78_RR R 60 ? R 78 ? R 63 ? R 77 ? 1 B A 56 1_555 B U 71 1_555 B C 57 1_555 B G 70 1_555 -1.505 0.017 3.231 2.546 10.481 54.297 -0.585 1.769 3.117 11.359 -2.759 55.278 27 RR_A63C64:G76U77_RR R 63 ? R 77 ? R 64 ? R 76 ? 1 B C 57 1_555 B G 70 1_555 B C 58 1_555 B G 69 1_555 -0.383 -1.654 3.976 -5.432 17.200 33.116 -5.062 -0.193 2.835 27.763 8.768 37.589 28 RR_C64C65:G75G76_RR R 64 ? R 76 ? R 65 ? R 75 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'MAGNESIUM ION' MG 5 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3MXH _pdbx_initial_refinement_model.details 'PDB entry 3MXH' #