data_3B5S # _entry.id 3B5S # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 3B5S pdb_00003b5s 10.2210/pdb3b5s/pdb NDB UR0132 ? ? RCSB RCSB045113 ? ? WWPDB D_1000045113 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2P7F ;The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme ; unspecified PDB 3B58 . unspecified PDB 3B5A . unspecified PDB 3B5F . unspecified PDB 3B91 . unspecified # _pdbx_database_status.entry_id 3B5S _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-10-26 _pdbx_database_status.SG_entry N _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'MacElrevey, C.' 1 'Krucinska, J.' 2 'Wedekind, J.E.' 3 # _citation.id primary _citation.title 'Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.' _citation.journal_abbrev Rna _citation.journal_volume 14 _citation.page_first 1600 _citation.page_last 1616 _citation.year 2008 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18596253 _citation.pdbx_database_id_DOI 10.1261/rna.1055308 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'MacElrevey, C.' 1 ? primary 'Salter, J.D.' 2 ? primary 'Krucinska, J.' 3 ? primary 'Wedekind, J.E.' 4 ? # _cell.entry_id 3B5S _cell.length_a 93.500 _cell.length_b 93.500 _cell.length_c 133.420 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 3B5S _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 178 _symmetry.cell_setting ? _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 syn 'Loop A Substrate strand' 4066.497 1 ? ? ? ;2'-O-methyl modification at residue 5 ; 2 polymer syn '29-mer Loop A and Loop B Ribozyme strand' 9762.989 1 ? ? ? 'Synthetic polyethylene glycol linker at hinge position 14' 3 polymer syn 'Loop B S-turn strand' 6006.583 1 ? 'A38(N6G), U39C' ? ? 4 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 5 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 6 water nat water 18.015 33 ? ? ? ? # 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 polyribonucleotide no yes 'UCCC(A2M)GUCCACCG' UCCCAGUCCACCG A ? 2 polyribonucleotide no yes 'CGGUGAGAAGGG(S9L)GGCAGAGAAACACACGA' CGGUGAGAAGGGXGGCAGAGAAACACACGA B ? 3 polyribonucleotide no yes 'UCGUGGU(N6G)CAUUACCUGCC' UCGUGGUGCAUUACCUGCC C ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 C n 1 3 C n 1 4 C n 1 5 A2M n 1 6 G n 1 7 U n 1 8 C n 1 9 C n 1 10 A n 1 11 C n 1 12 C n 1 13 G n 2 1 C n 2 2 G n 2 3 G n 2 4 U n 2 5 G n 2 6 A n 2 7 G n 2 8 A n 2 9 A n 2 10 G n 2 11 G n 2 12 G n 2 13 S9L n 2 14 G n 2 15 G n 2 16 C n 2 17 A n 2 18 G n 2 19 A n 2 20 G n 2 21 A n 2 22 A n 2 23 A n 2 24 C n 2 25 A n 2 26 C n 2 27 A n 2 28 C n 2 29 G n 2 30 A n 3 1 U n 3 2 C n 3 3 G n 3 4 U n 3 5 G n 3 6 G n 3 7 U n 3 8 N6G n 3 9 C n 3 10 A n 3 11 U n 3 12 U n 3 13 A n 3 14 C n 3 15 C n 3 16 U n 3 17 G n 3 18 C n 3 19 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'solid-phase synthesis at Keck Institute, Yale' 2 1 sample ? ? ? ? ? 'solid phase chemical synthesis at Dharmacon, Colorado' 3 1 sample ? ? ? ? ? 'solid phase chemical synthesis at Dharmacon, Colorado' # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 PDB 3B58 3B58 1 'UCCC(A2M)GUCCACCG' ? 2 2 PDB 3B58 3B58 1 'CGGUGAGAAGGG(S9L)GGCAGAGAAACACACGA' ? 3 3 PDB 3B58 3B58 1 'UCGUGGU(N6G)CAUUACCUGCC' ? # 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 3B5S A 1 ? 13 ? 3B58 1 ? 13 ? 1 13 2 2 3B5S B 1 ? 30 ? 3B58 1 ? 30 ? 2 31 3 3 3B5S C 1 ? 19 ? 3B58 1 ? 19 ? 31 49 # 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 A2M 'RNA linking' n ;2'-O-methyladenosine 5'-(dihydrogen phosphate) ; ? 'C11 H16 N5 O7 P' 361.248 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 HOH non-polymer . WATER ? 'H2 O' 18.015 N6G 'RNA linking' n '((2R,3S,4R,5S)-5-(2,6-DIAMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE' ? 'C10 H15 N6 O7 P' 362.236 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 S9L non-polymer . '2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE' ? 'C6 H15 O7 P' 230.153 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 3B5S _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.24 _exptl_crystal.density_percent_sol 78. _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 293 _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;PEG 2K MME, lithium sulfate, sodium cacodylate, spermidine, cobalt hexaammine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 'PEG 2K MME' ? ? ? 1 2 1 Li2SO4 ? ? ? 1 3 1 'sodium cacodylate' ? ? ? 1 4 1 spermidine ? ? ? 1 5 1 'cobalt hexaammine' ? ? ? 1 6 2 'PEG 2K MME' ? ? ? 1 7 2 Li2SO4 ? ? ? 1 8 2 spermidine ? ? ? # _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 210' _diffrn_detector.pdbx_collection_date 2006-09-30 _diffrn_detector.details 'BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'horizontal focusing 5.05 degree asymmetric cut 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 0.977 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'CHESS BEAMLINE A1' _diffrn_source.pdbx_synchrotron_site CHESS _diffrn_source.pdbx_synchrotron_beamline A1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.977 # _reflns.entry_id 3B5S _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 40.49 _reflns.d_resolution_high 2.25 _reflns.number_obs 16724 _reflns.number_all 16976 _reflns.percent_possible_obs 98.5 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.037 _reflns.pdbx_netI_over_sigmaI 25.5 _reflns.B_iso_Wilson_estimate 113.4 _reflns.pdbx_redundancy 7.8 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.25 _reflns_shell.d_res_low 2.35 _reflns_shell.percent_possible_all 98.1 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value .476 _reflns_shell.meanI_over_sigI_obs 3.5 _reflns_shell.pdbx_redundancy 8.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1615 _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 3B5S _refine.ls_number_reflns_obs 16669 _refine.ls_number_reflns_all 16976 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F -3.0 _refine.pdbx_data_cutoff_high_absF 860219.44 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 40.49 _refine.ls_d_res_high 2.25 _refine.ls_percent_reflns_obs 98.1 _refine.ls_R_factor_obs 0.223 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.223 _refine.ls_R_factor_R_free 0.241 _refine.ls_R_factor_R_free_error 0.006 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 1669 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 71.1 _refine.aniso_B[1][1] -7.78 _refine.aniso_B[2][2] -7.78 _refine.aniso_B[3][3] 15.56 _refine.aniso_B[1][2] -6.36 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.32 _refine.solvent_model_param_bsol 58 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'Alternate conformation at U1 of chain A' _refine.pdbx_starting_model 2OUE _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _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_analyze.entry_id 3B5S _refine_analyze.Luzzati_coordinate_error_obs 0.49 _refine_analyze.Luzzati_sigma_a_obs 0.42 _refine_analyze.Luzzati_d_res_low_obs 40.49 _refine_analyze.Luzzati_coordinate_error_free 0.55 _refine_analyze.Luzzati_sigma_a_free 0.46 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1312 _refine_hist.pdbx_number_atoms_ligand 19 _refine_hist.number_atoms_solvent 33 _refine_hist.number_atoms_total 1364 _refine_hist.d_res_high 2.25 _refine_hist.d_res_low 40.49 # 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_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.6 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 17.6 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.85 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 4 _refine_ls_shell.d_res_high 2.25 _refine_ls_shell.d_res_low 2.48 _refine_ls_shell.number_reflns_R_work 3645 _refine_ls_shell.R_factor_R_work 0.482 _refine_ls_shell.percent_reflns_obs 98.0 _refine_ls_shell.R_factor_R_free 0.517 _refine_ls_shell.R_factor_R_free_error 0.026 _refine_ls_shell.percent_reflns_R_free 9.9 _refine_ls_shell.number_reflns_R_free 402 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 3645 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 water_rep.param dna-rna0107.top 'X-RAY DIFFRACTION' 2 dna-rna0107.par water.top 'X-RAY DIFFRACTION' 3 cobalt.par cobalt.top 'X-RAY DIFFRACTION' 4 ion.param ion.top 'X-RAY DIFFRACTION' # _struct.entry_id 3B5S _struct.title ;Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'-O-methyl Modification at the Active Site ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3B5S _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;hairpin ribozyme; RNA; 2, 6 diaminopurine; 2'-O-methyl, RNA ; # 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 6 ? H N N 6 ? I N N 6 ? # _struct_biol.id 1 _struct_biol.details ? # 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 ? A C 4 "O3'" ? ? ? 1_555 A A2M 5 P ? ? A C 4 A A2M 5 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale2 covale one ? A A2M 5 "O3'" ? ? ? 1_555 A G 6 P ? ? A A2M 5 A G 6 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale3 covale both ? B G 12 "O3'" ? ? ? 1_555 B S9L 13 P ? ? B G 13 B S9L 14 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale4 covale both ? B S9L 13 "O3'" ? ? ? 1_555 B G 14 P ? ? B S9L 14 B G 15 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale5 covale both ? C U 7 "O3'" ? ? ? 1_555 C N6G 8 P ? ? C U 37 C N6G 38 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale6 covale both ? C N6G 8 "O3'" ? ? ? 1_555 C C 9 P ? ? C N6G 38 C C 39 1_555 ? ? ? ? ? ? ? 1.606 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A2M 5 N3 ? ? ? 1_555 B A 8 N6 ? ? A A2M 5 B A 9 1_555 ? ? ? ? ? ? 'A2M-A MISPAIR' ? ? ? hydrog11 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 24 N3 ? ? A G 6 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 24 O2 ? ? A G 6 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 24 N4 ? ? A G 6 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 O4 ? ? ? 1_555 B G 7 N2 ? ? A U 7 B G 8 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog15 hydrog ? ? A C 8 N4 ? ? ? 1_555 B A 6 N1 ? ? A C 8 B A 7 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog16 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 9 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 9 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 9 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 10 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 10 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 13 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 13 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 13 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B G 14 N1 ? ? ? 1_555 C C 19 N3 ? ? B G 15 C C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B G 14 N2 ? ? ? 1_555 C C 19 O2 ? ? B G 15 C C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B G 14 O6 ? ? ? 1_555 C C 19 N4 ? ? B G 15 C C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B G 15 N1 ? ? ? 1_555 C C 18 N3 ? ? B G 16 C C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B G 15 N2 ? ? ? 1_555 C C 18 O2 ? ? B G 16 C C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 15 O6 ? ? ? 1_555 C C 18 N4 ? ? B G 16 C C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B C 16 N3 ? ? ? 1_555 C G 17 N1 ? ? B C 17 C G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B C 16 N4 ? ? ? 1_555 C G 17 O6 ? ? B C 17 C G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B C 16 O2 ? ? ? 1_555 C G 17 N2 ? ? B C 17 C G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B A 17 N1 ? ? ? 1_555 C U 16 N3 ? ? B A 18 C U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B A 17 N6 ? ? ? 1_555 C U 16 O4 ? ? B A 18 C U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B G 18 N1 ? ? ? 1_555 C C 15 N3 ? ? B G 19 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B G 18 N2 ? ? ? 1_555 C C 15 O2 ? ? B G 19 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B G 18 O6 ? ? ? 1_555 C C 15 N4 ? ? B G 19 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B A 19 N1 ? ? ? 1_555 C C 14 N4 ? ? B A 20 C C 44 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog45 hydrog ? ? B G 20 N2 ? ? ? 1_555 C A 13 N7 ? ? B G 21 C A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog46 hydrog ? ? B G 20 N3 ? ? ? 1_555 C A 13 N6 ? ? B G 21 C A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog47 hydrog ? ? B A 21 N6 ? ? ? 1_555 C U 11 O2 ? ? B A 22 C U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog48 hydrog ? ? B A 21 N7 ? ? ? 1_555 C U 11 N3 ? ? B A 22 C U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog49 hydrog ? ? B A 22 N6 ? ? ? 1_555 C A 10 N1 ? ? B A 23 C A 40 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog50 hydrog ? ? B A 22 N7 ? ? ? 1_555 C A 10 N6 ? ? B A 23 C A 40 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog51 hydrog ? ? B A 23 N6 ? ? ? 1_555 C N6G 8 N7 ? ? B A 24 C N6G 38 1_555 ? ? ? ? ? ? 'A-N6G MISPAIR' ? ? ? hydrog52 hydrog ? ? B A 25 N1 ? ? ? 1_555 C G 6 N1 ? ? B A 26 C G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog53 hydrog ? ? B A 25 N6 ? ? ? 1_555 C G 6 O6 ? ? B A 26 C G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog54 hydrog ? ? B C 26 N3 ? ? ? 1_555 C G 5 N1 ? ? B C 27 C G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B C 26 N4 ? ? ? 1_555 C G 5 O6 ? ? B C 27 C G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B C 26 O2 ? ? ? 1_555 C G 5 N2 ? ? B C 27 C G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B A 27 N1 ? ? ? 1_555 C U 4 N3 ? ? B A 28 C U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B A 27 N6 ? ? ? 1_555 C U 4 O4 ? ? B A 28 C U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B C 28 N3 ? ? ? 1_555 C G 3 N1 ? ? B C 29 C G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? B C 28 N4 ? ? ? 1_555 C G 3 O6 ? ? B C 29 C G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B C 28 O2 ? ? ? 1_555 C G 3 N2 ? ? B C 29 C G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? B G 29 N1 ? ? ? 1_555 C C 2 N3 ? ? B G 30 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? B G 29 N2 ? ? ? 1_555 C C 2 O2 ? ? B G 30 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? B G 29 O6 ? ? ? 1_555 C C 2 N4 ? ? B G 30 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? B A 30 N1 ? ? ? 1_555 C U 1 N3 ? ? B A 31 C U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? B A 30 N6 ? ? ? 1_555 C U 1 O4 ? ? B A 31 C U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 3B5S _atom_sites.fract_transf_matrix[1][1] 0.010695 _atom_sites.fract_transf_matrix[1][2] 0.006175 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.012350 _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] 0.007495 _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 CO 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 U 1 1 1 U U A . n A 1 2 C 2 2 2 C C A . n A 1 3 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 A2M 5 5 5 A2M A2M A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 G G A . n B 2 1 C 1 2 2 C C B . n B 2 2 G 2 3 3 G G B . n B 2 3 G 3 4 4 G G B . n B 2 4 U 4 5 5 U U B . n B 2 5 G 5 6 6 G G B . n B 2 6 A 6 7 7 A A B . n B 2 7 G 7 8 8 G G B . n B 2 8 A 8 9 9 A A B . n B 2 9 A 9 10 10 A A B . n B 2 10 G 10 11 11 G G B . n B 2 11 G 11 12 12 G G B . n B 2 12 G 12 13 13 G G B . n B 2 13 S9L 13 14 14 S9L S9L B . n B 2 14 G 14 15 15 G G B . n B 2 15 G 15 16 16 G G B . n B 2 16 C 16 17 17 C C B . n B 2 17 A 17 18 18 A A B . n B 2 18 G 18 19 19 G G B . n B 2 19 A 19 20 20 A A B . n B 2 20 G 20 21 21 G G B . n B 2 21 A 21 22 22 A A B . n B 2 22 A 22 23 23 A A B . n B 2 23 A 23 24 24 A A B . n B 2 24 C 24 25 25 C C B . n B 2 25 A 25 26 26 A A B . n B 2 26 C 26 27 27 C C B . n B 2 27 A 27 28 28 A A B . n B 2 28 C 28 29 29 C C B . n B 2 29 G 29 30 30 G G B . n B 2 30 A 30 31 31 A A B . n C 3 1 U 1 31 31 U U C . n C 3 2 C 2 32 32 C C C . n C 3 3 G 3 33 33 G G C . n C 3 4 U 4 34 34 U U C . n C 3 5 G 5 35 35 G G C . n C 3 6 G 6 36 36 G G C . n C 3 7 U 7 37 37 U U C . n C 3 8 N6G 8 38 38 N6G N6G C . n C 3 9 C 9 39 39 C C C . n C 3 10 A 10 40 40 A A C . n C 3 11 U 11 41 41 U U C . n C 3 12 U 12 42 42 U U C . n C 3 13 A 13 43 43 A A C . n C 3 14 C 14 44 44 C C C . n C 3 15 C 15 45 45 C C C . n C 3 16 U 16 46 46 U U C . n C 3 17 G 17 47 47 G G C . n C 3 18 C 18 48 48 C C C . n C 3 19 C 19 49 49 C C C . 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 SO4 1 103 103 SO4 SO4 A . E 5 NCO 1 102 102 NCO NCO B . F 5 NCO 1 101 101 NCO NCO C . G 6 HOH 1 104 1 HOH HOH A . G 6 HOH 2 105 13 HOH HOH A . G 6 HOH 3 106 14 HOH HOH A . G 6 HOH 4 107 15 HOH HOH A . G 6 HOH 5 108 20 HOH HOH A . H 6 HOH 1 103 5 HOH HOH B . H 6 HOH 2 104 7 HOH HOH B . H 6 HOH 3 105 9 HOH HOH B . H 6 HOH 4 106 10 HOH HOH B . H 6 HOH 5 107 16 HOH HOH B . H 6 HOH 6 108 17 HOH HOH B . H 6 HOH 7 109 18 HOH HOH B . H 6 HOH 8 110 22 HOH HOH B . H 6 HOH 9 111 25 HOH HOH B . H 6 HOH 10 112 27 HOH HOH B . H 6 HOH 11 113 28 HOH HOH B . H 6 HOH 12 114 29 HOH HOH B . H 6 HOH 13 115 30 HOH HOH B . H 6 HOH 14 116 32 HOH HOH B . I 6 HOH 1 102 52 HOH HOH C . I 6 HOH 2 103 3 HOH HOH C . I 6 HOH 3 104 4 HOH HOH C . I 6 HOH 4 105 6 HOH HOH C . I 6 HOH 5 106 8 HOH HOH C . I 6 HOH 6 107 11 HOH HOH C . I 6 HOH 7 108 12 HOH HOH C . I 6 HOH 8 109 19 HOH HOH C . I 6 HOH 9 110 21 HOH HOH C . I 6 HOH 10 111 23 HOH HOH C . I 6 HOH 11 112 24 HOH HOH C . I 6 HOH 12 113 26 HOH HOH C . I 6 HOH 13 114 31 HOH HOH C . I 6 HOH 14 115 33 HOH HOH C . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A A2M 5 A A2M 5 ? A "2'-O-METHYL-ADENOSINE-5'-MONOPHOSPHATE" 2 C N6G 8 C N6G 38 ? G ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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,H,I # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 6710 ? 1 MORE -31 ? 1 'SSA (A^2)' 9140 ? # _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_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 2008-08-12 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2023-08-30 # _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' 'Non-polymer description' 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Refinement description' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 4 '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' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_initial_refinement_model 6 4 'Structure model' struct_conn # 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' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal Adxv 'data processing' . ? 1 CNS refinement . ? 2 CrystalClear 'data reduction' . ? 3 CrystalClear 'data scaling' . ? 4 CNS phasing . ? 5 # 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'" A C 4 ? ? "C1'" A C 4 ? ? N1 A C 4 ? ? 112.97 108.50 4.47 0.70 N 2 1 "O4'" C U 37 ? ? "C1'" C U 37 ? ? N1 C U 37 ? ? 113.57 108.50 5.07 0.70 N # 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 A2M P P N N 38 A2M OP1 O N N 39 A2M OP3 O N N 40 A2M "O5'" O N N 41 A2M "C5'" C N N 42 A2M "C4'" C N R 43 A2M "O4'" O N N 44 A2M "C3'" C N R 45 A2M "O3'" O N N 46 A2M "C2'" C N R 47 A2M "O2'" O N N 48 A2M "C1'" C N R 49 A2M "CM'" C N N 50 A2M N9 N Y N 51 A2M C8 C Y N 52 A2M N7 N Y N 53 A2M C5 C Y N 54 A2M C6 C Y N 55 A2M N6 N N N 56 A2M N1 N Y N 57 A2M C2 C Y N 58 A2M N3 N Y N 59 A2M C4 C Y N 60 A2M HOP3 H N N 61 A2M "H5'" H N N 62 A2M "H5''" H N N 63 A2M "H4'" H N N 64 A2M "H3'" H N N 65 A2M "HO3'" H N N 66 A2M "H2'" H N N 67 A2M "H1'" H N N 68 A2M "HM'1" H N N 69 A2M "HM'2" H N N 70 A2M "HM'3" H N N 71 A2M H8 H N N 72 A2M H61 H N N 73 A2M H62 H N N 74 A2M H2 H N N 75 A2M OP2 O N N 76 A2M HOP2 H N N 77 C OP3 O N N 78 C P P N N 79 C OP1 O N N 80 C OP2 O N N 81 C "O5'" O N N 82 C "C5'" C N N 83 C "C4'" C N R 84 C "O4'" O N N 85 C "C3'" C N S 86 C "O3'" O N N 87 C "C2'" C N R 88 C "O2'" O N N 89 C "C1'" C N R 90 C N1 N N N 91 C C2 C N N 92 C O2 O N N 93 C N3 N N N 94 C C4 C N N 95 C N4 N N N 96 C C5 C N N 97 C C6 C N N 98 C HOP3 H N N 99 C HOP2 H N N 100 C "H5'" H N N 101 C "H5''" H N N 102 C "H4'" H N N 103 C "H3'" H N N 104 C "HO3'" H N N 105 C "H2'" H N N 106 C "HO2'" H N N 107 C "H1'" H N N 108 C H41 H N N 109 C H42 H N N 110 C H5 H N N 111 C H6 H N N 112 G OP3 O N N 113 G P P N N 114 G OP1 O N N 115 G OP2 O N N 116 G "O5'" O N N 117 G "C5'" C N N 118 G "C4'" C N R 119 G "O4'" O N N 120 G "C3'" C N S 121 G "O3'" O N N 122 G "C2'" C N R 123 G "O2'" O N N 124 G "C1'" C N R 125 G N9 N Y N 126 G C8 C Y N 127 G N7 N Y N 128 G C5 C Y N 129 G C6 C N N 130 G O6 O N N 131 G N1 N N N 132 G C2 C N N 133 G N2 N N N 134 G N3 N N N 135 G C4 C Y N 136 G HOP3 H N N 137 G HOP2 H N N 138 G "H5'" H N N 139 G "H5''" H N N 140 G "H4'" H N N 141 G "H3'" H N N 142 G "HO3'" H N N 143 G "H2'" H N N 144 G "HO2'" H N N 145 G "H1'" H N N 146 G H8 H N N 147 G H1 H N N 148 G H21 H N N 149 G H22 H N N 150 HOH O O N N 151 HOH H1 H N N 152 HOH H2 H N N 153 N6G P P N N 154 N6G OP1 O N N 155 N6G OP2 O N N 156 N6G "O5'" O N N 157 N6G "C5'" C N N 158 N6G "C4'" C N R 159 N6G "O4'" O N N 160 N6G "C1'" C N R 161 N6G N9 N Y N 162 N6G C4 C Y N 163 N6G N3 N Y N 164 N6G C2 C Y N 165 N6G N2 N N N 166 N6G N1 N Y N 167 N6G C6 C Y N 168 N6G N6 N N N 169 N6G C5 C Y N 170 N6G N7 N Y N 171 N6G C8 C Y N 172 N6G "C2'" C N R 173 N6G "O2'" O N N 174 N6G "C3'" C N S 175 N6G "O3'" O N N 176 N6G OP3 O N N 177 N6G HOP2 H N N 178 N6G "H5'" H N N 179 N6G "H5''" H N N 180 N6G "H4'" H N N 181 N6G "H1'" H N N 182 N6G HN21 H N N 183 N6G HN22 H N N 184 N6G HN61 H N N 185 N6G HN62 H N N 186 N6G H8 H N N 187 N6G "H2'" H N N 188 N6G "HO2'" H N N 189 N6G "H3'" H N N 190 N6G "HO3'" H N N 191 N6G HOP3 H N N 192 NCO CO CO N N 193 NCO N1 N N N 194 NCO N2 N N N 195 NCO N3 N N N 196 NCO N4 N N N 197 NCO N5 N N N 198 NCO N6 N N N 199 NCO HN11 H N N 200 NCO HN12 H N N 201 NCO HN13 H N N 202 NCO HN21 H N N 203 NCO HN22 H N N 204 NCO HN23 H N N 205 NCO HN31 H N N 206 NCO HN32 H N N 207 NCO HN33 H N N 208 NCO HN41 H N N 209 NCO HN42 H N N 210 NCO HN43 H N N 211 NCO HN51 H N N 212 NCO HN52 H N N 213 NCO HN53 H N N 214 NCO HN61 H N N 215 NCO HN62 H N N 216 NCO HN63 H N N 217 S9L O3P O N N 218 S9L P P N N 219 S9L O1P O N N 220 S9L O2P O N N 221 S9L "O5'" O N N 222 S9L C12 C N N 223 S9L C22 C N N 224 S9L OH3 O N N 225 S9L C13 C N N 226 S9L C23 C N N 227 S9L OH4 O N N 228 S9L C14 C N N 229 S9L C24 C N N 230 S9L "O3'" O N N 231 S9L HO3P H N N 232 S9L HO1P H N N 233 S9L H121 H N N 234 S9L H122 H N N 235 S9L H221 H N N 236 S9L H222 H N N 237 S9L H131 H N N 238 S9L H132 H N N 239 S9L H231 H N N 240 S9L H232 H N N 241 S9L H141 H N N 242 S9L H142 H N N 243 S9L H241 H N N 244 S9L H242 H N N 245 S9L "HO3'" H N N 246 SO4 S S N N 247 SO4 O1 O N N 248 SO4 O2 O N N 249 SO4 O3 O N N 250 SO4 O4 O N N 251 U OP3 O N N 252 U P P N N 253 U OP1 O N N 254 U OP2 O N N 255 U "O5'" O N N 256 U "C5'" C N N 257 U "C4'" C N R 258 U "O4'" O N N 259 U "C3'" C N S 260 U "O3'" O N N 261 U "C2'" C N R 262 U "O2'" O N N 263 U "C1'" C N R 264 U N1 N N N 265 U C2 C N N 266 U O2 O N N 267 U N3 N N N 268 U C4 C N N 269 U O4 O N N 270 U C5 C N N 271 U C6 C N N 272 U HOP3 H N N 273 U HOP2 H N N 274 U "H5'" H N N 275 U "H5''" H N N 276 U "H4'" H N N 277 U "H3'" H N N 278 U "HO3'" H N N 279 U "H2'" H N N 280 U "HO2'" H N N 281 U "H1'" H N N 282 U H3 H N N 283 U H5 H N N 284 U H6 H N N 285 # 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 A2M P OP1 doub N N 40 A2M P OP3 sing N N 41 A2M P "O5'" sing N N 42 A2M OP3 HOP3 sing N N 43 A2M "O5'" "C5'" sing N N 44 A2M "C5'" "C4'" sing N N 45 A2M "C5'" "H5'" sing N N 46 A2M "C5'" "H5''" sing N N 47 A2M "C4'" "O4'" sing N N 48 A2M "C4'" "C3'" sing N N 49 A2M "C4'" "H4'" sing N N 50 A2M "O4'" "C1'" sing N N 51 A2M "C3'" "O3'" sing N N 52 A2M "C3'" "C2'" sing N N 53 A2M "C3'" "H3'" sing N N 54 A2M "O3'" "HO3'" sing N N 55 A2M "C2'" "O2'" sing N N 56 A2M "C2'" "C1'" sing N N 57 A2M "C2'" "H2'" sing N N 58 A2M "O2'" "CM'" sing N N 59 A2M "C1'" N9 sing N N 60 A2M "C1'" "H1'" sing N N 61 A2M "CM'" "HM'1" sing N N 62 A2M "CM'" "HM'2" sing N N 63 A2M "CM'" "HM'3" sing N N 64 A2M N9 C8 sing Y N 65 A2M N9 C4 sing Y N 66 A2M C8 N7 doub Y N 67 A2M C8 H8 sing N N 68 A2M N7 C5 sing Y N 69 A2M C5 C6 sing Y N 70 A2M C5 C4 doub Y N 71 A2M C6 N6 sing N N 72 A2M C6 N1 doub Y N 73 A2M N6 H61 sing N N 74 A2M N6 H62 sing N N 75 A2M N1 C2 sing Y N 76 A2M C2 N3 doub Y N 77 A2M C2 H2 sing N N 78 A2M N3 C4 sing Y N 79 A2M P OP2 sing N N 80 A2M OP2 HOP2 sing N N 81 C OP3 P sing N N 82 C OP3 HOP3 sing N N 83 C P OP1 doub N N 84 C P OP2 sing N N 85 C P "O5'" sing N N 86 C OP2 HOP2 sing N N 87 C "O5'" "C5'" sing N N 88 C "C5'" "C4'" sing N N 89 C "C5'" "H5'" sing N N 90 C "C5'" "H5''" sing N N 91 C "C4'" "O4'" sing N N 92 C "C4'" "C3'" sing N N 93 C "C4'" "H4'" sing N N 94 C "O4'" "C1'" sing N N 95 C "C3'" "O3'" sing N N 96 C "C3'" "C2'" sing N N 97 C "C3'" "H3'" sing N N 98 C "O3'" "HO3'" sing N N 99 C "C2'" "O2'" sing N N 100 C "C2'" "C1'" sing N N 101 C "C2'" "H2'" sing N N 102 C "O2'" "HO2'" sing N N 103 C "C1'" N1 sing N N 104 C "C1'" "H1'" sing N N 105 C N1 C2 sing N N 106 C N1 C6 sing N N 107 C C2 O2 doub N N 108 C C2 N3 sing N N 109 C N3 C4 doub N N 110 C C4 N4 sing N N 111 C C4 C5 sing N N 112 C N4 H41 sing N N 113 C N4 H42 sing N N 114 C C5 C6 doub N N 115 C C5 H5 sing N N 116 C C6 H6 sing N N 117 G OP3 P sing N N 118 G OP3 HOP3 sing N N 119 G P OP1 doub N N 120 G P OP2 sing N N 121 G P "O5'" sing N N 122 G OP2 HOP2 sing N N 123 G "O5'" "C5'" sing N N 124 G "C5'" "C4'" sing N N 125 G "C5'" "H5'" sing N N 126 G "C5'" "H5''" sing N N 127 G "C4'" "O4'" sing N N 128 G "C4'" "C3'" sing N N 129 G "C4'" "H4'" sing N N 130 G "O4'" "C1'" sing N N 131 G "C3'" "O3'" sing N N 132 G "C3'" "C2'" sing N N 133 G "C3'" "H3'" sing N N 134 G "O3'" "HO3'" sing N N 135 G "C2'" "O2'" sing N N 136 G "C2'" "C1'" sing N N 137 G "C2'" "H2'" sing N N 138 G "O2'" "HO2'" sing N N 139 G "C1'" N9 sing N N 140 G "C1'" "H1'" sing N N 141 G N9 C8 sing Y N 142 G N9 C4 sing Y N 143 G C8 N7 doub Y N 144 G C8 H8 sing N N 145 G N7 C5 sing Y N 146 G C5 C6 sing N N 147 G C5 C4 doub Y N 148 G C6 O6 doub N N 149 G C6 N1 sing N N 150 G N1 C2 sing N N 151 G N1 H1 sing N N 152 G C2 N2 sing N N 153 G C2 N3 doub N N 154 G N2 H21 sing N N 155 G N2 H22 sing N N 156 G N3 C4 sing N N 157 HOH O H1 sing N N 158 HOH O H2 sing N N 159 N6G P OP1 doub N N 160 N6G P OP2 sing N N 161 N6G P "O5'" sing N N 162 N6G P OP3 sing N N 163 N6G OP2 HOP2 sing N N 164 N6G "O5'" "C5'" sing N N 165 N6G "C5'" "C4'" sing N N 166 N6G "C5'" "H5'" sing N N 167 N6G "C5'" "H5''" sing N N 168 N6G "C4'" "O4'" sing N N 169 N6G "C4'" "C3'" sing N N 170 N6G "C4'" "H4'" sing N N 171 N6G "O4'" "C1'" sing N N 172 N6G "C1'" N9 sing N N 173 N6G "C1'" "C2'" sing N N 174 N6G "C1'" "H1'" sing N N 175 N6G N9 C4 sing Y N 176 N6G N9 C8 sing Y N 177 N6G C4 N3 sing Y N 178 N6G C4 C5 doub Y N 179 N6G N3 C2 doub Y N 180 N6G C2 N2 sing N N 181 N6G C2 N1 sing Y N 182 N6G N2 HN21 sing N N 183 N6G N2 HN22 sing N N 184 N6G N1 C6 doub Y N 185 N6G C6 N6 sing N N 186 N6G C6 C5 sing Y N 187 N6G N6 HN61 sing N N 188 N6G N6 HN62 sing N N 189 N6G C5 N7 sing Y N 190 N6G N7 C8 doub Y N 191 N6G C8 H8 sing N N 192 N6G "C2'" "O2'" sing N N 193 N6G "C2'" "C3'" sing N N 194 N6G "C2'" "H2'" sing N N 195 N6G "O2'" "HO2'" sing N N 196 N6G "C3'" "O3'" sing N N 197 N6G "C3'" "H3'" sing N N 198 N6G "O3'" "HO3'" sing N N 199 N6G OP3 HOP3 sing N N 200 NCO CO N1 sing N N 201 NCO CO N2 sing N N 202 NCO CO N3 sing N N 203 NCO CO N4 sing N N 204 NCO CO N5 sing N N 205 NCO CO N6 sing N N 206 NCO N1 HN11 sing N N 207 NCO N1 HN12 sing N N 208 NCO N1 HN13 sing N N 209 NCO N2 HN21 sing N N 210 NCO N2 HN22 sing N N 211 NCO N2 HN23 sing N N 212 NCO N3 HN31 sing N N 213 NCO N3 HN32 sing N N 214 NCO N3 HN33 sing N N 215 NCO N4 HN41 sing N N 216 NCO N4 HN42 sing N N 217 NCO N4 HN43 sing N N 218 NCO N5 HN51 sing N N 219 NCO N5 HN52 sing N N 220 NCO N5 HN53 sing N N 221 NCO N6 HN61 sing N N 222 NCO N6 HN62 sing N N 223 NCO N6 HN63 sing N N 224 S9L O3P P sing N N 225 S9L O3P HO3P sing N N 226 S9L P O2P doub N N 227 S9L P O1P sing N N 228 S9L P "O5'" sing N N 229 S9L O1P HO1P sing N N 230 S9L "O5'" C12 sing N N 231 S9L C12 C22 sing N N 232 S9L C12 H121 sing N N 233 S9L C12 H122 sing N N 234 S9L C22 OH3 sing N N 235 S9L C22 H221 sing N N 236 S9L C22 H222 sing N N 237 S9L OH3 C23 sing N N 238 S9L C13 C23 sing N N 239 S9L C13 OH4 sing N N 240 S9L C13 H131 sing N N 241 S9L C13 H132 sing N N 242 S9L C23 H231 sing N N 243 S9L C23 H232 sing N N 244 S9L OH4 C24 sing N N 245 S9L C14 C24 sing N N 246 S9L C14 "O3'" sing N N 247 S9L C14 H141 sing N N 248 S9L C14 H142 sing N N 249 S9L C24 H241 sing N N 250 S9L C24 H242 sing N N 251 S9L "O3'" "HO3'" sing N N 252 SO4 S O1 doub N N 253 SO4 S O2 doub N N 254 SO4 S O3 sing N N 255 SO4 S O4 sing N N 256 U OP3 P sing N N 257 U OP3 HOP3 sing N N 258 U P OP1 doub N N 259 U P OP2 sing N N 260 U P "O5'" sing N N 261 U OP2 HOP2 sing N N 262 U "O5'" "C5'" sing N N 263 U "C5'" "C4'" sing N N 264 U "C5'" "H5'" sing N N 265 U "C5'" "H5''" sing N N 266 U "C4'" "O4'" sing N N 267 U "C4'" "C3'" sing N N 268 U "C4'" "H4'" sing N N 269 U "O4'" "C1'" sing N N 270 U "C3'" "O3'" sing N N 271 U "C3'" "C2'" sing N N 272 U "C3'" "H3'" sing N N 273 U "O3'" "HO3'" sing N N 274 U "C2'" "O2'" sing N N 275 U "C2'" "C1'" sing N N 276 U "C2'" "H2'" sing N N 277 U "O2'" "HO2'" sing N N 278 U "C1'" N1 sing N N 279 U "C1'" "H1'" sing N N 280 U N1 C2 sing N N 281 U N1 C6 sing N N 282 U C2 O2 doub N N 283 U C2 N3 sing N N 284 U N3 C4 sing N N 285 U N3 H3 sing N N 286 U C4 O4 doub N N 287 U C4 C5 sing N N 288 U C5 C6 doub N N 289 U C5 H5 sing N N 290 U C6 H6 sing N N 291 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3B5S 'double helix' 3B5S 'a-form double helix' 3B5S 'mismatched base pair' 3B5S 'internal loop' # 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 A C 2 1_555 B G 12 1_555 0.255 -0.096 -0.305 8.032 -17.303 2.830 1 A_C2:G13_B A 2 ? B 13 ? 19 1 1 A C 3 1_555 B G 11 1_555 0.270 -0.192 -0.093 -0.642 -6.391 -1.496 2 A_C3:G12_B A 3 ? B 12 ? 19 1 1 A C 4 1_555 B G 10 1_555 0.412 -0.161 -0.066 4.395 -2.903 2.921 3 A_C4:G11_B A 4 ? B 11 ? 19 1 1 A A2M 5 1_555 B A 8 1_555 6.763 -3.897 -0.299 15.560 9.240 -26.921 4 A_A2M5:A9_B A 5 ? B 9 ? ? ? 1 A U 7 1_555 B G 7 1_555 -7.741 -2.837 -0.317 13.221 0.038 1.901 5 A_U7:G8_B A 7 ? B 8 ? ? ? 1 A C 8 1_555 B A 6 1_555 -2.096 0.458 -0.829 22.721 -13.217 10.311 6 A_C8:A7_B A 8 ? B 7 ? ? ? 1 A C 9 1_555 B G 5 1_555 0.032 0.046 -0.218 13.766 -14.007 6.628 7 A_C9:G6_B A 9 ? B 6 ? 19 1 1 A A 10 1_555 B U 4 1_555 0.273 -0.035 0.348 0.972 -11.083 7.369 8 A_A10:U5_B A 10 ? B 5 ? 20 1 1 A C 11 1_555 B G 3 1_555 0.236 -0.027 0.425 2.119 -12.679 4.331 9 A_C11:G4_B A 11 ? B 4 ? 19 1 1 A C 12 1_555 B G 2 1_555 0.289 -0.148 0.205 2.871 -11.935 4.703 10 A_C12:G3_B A 12 ? B 3 ? 19 1 1 A G 13 1_555 B C 1 1_555 -0.290 0.073 0.054 -3.055 -9.300 8.191 11 A_G13:C2_B A 13 ? B 2 ? 19 1 1 B G 14 1_555 C C 19 1_555 -0.328 -0.178 0.334 0.513 -8.980 -0.373 12 B_G15:C49_C B 15 ? C 49 ? 19 1 1 B G 15 1_555 C C 18 1_555 -0.203 -0.179 0.561 12.377 -8.916 -2.478 13 B_G16:C48_C B 16 ? C 48 ? 19 1 1 B C 16 1_555 C G 17 1_555 0.181 -0.064 -0.016 8.850 -12.271 -0.738 14 B_C17:G47_C B 17 ? C 47 ? 19 1 1 B A 17 1_555 C U 16 1_555 0.000 -0.080 -0.182 -3.089 -10.215 5.169 15 B_A18:U46_C B 18 ? C 46 ? 20 1 1 B G 18 1_555 C C 15 1_555 -0.305 -0.185 -0.480 -9.557 -9.288 5.654 16 B_G19:C45_C B 19 ? C 45 ? 19 1 1 B A 19 1_555 C C 14 1_555 2.298 0.275 -0.360 -15.219 -6.148 16.505 17 B_A20:C44_C B 20 ? C 44 ? ? 1 1 B G 20 1_555 C A 13 1_555 7.030 -4.545 -0.179 -6.516 1.408 -9.019 18 B_G21:A43_C B 21 ? C 43 ? 11 10 1 B A 21 1_555 C U 11 1_555 -4.168 -1.670 -0.255 -2.845 -10.376 -104.077 19 B_A22:U41_C B 22 ? C 41 ? 24 4 1 B A 22 1_555 C A 10 1_555 -4.232 1.215 -0.489 -0.949 -23.363 -99.979 20 B_A23:A40_C B 23 ? C 40 ? 5 4 1 B A 23 1_555 C N6G 8 1_555 5.227 3.401 -0.387 -4.198 -9.729 -155.851 21 B_A24:N6G38_C B 24 ? C 38 ? ? ? 1 B C 24 1_555 A G 6 1_555 0.118 -0.113 0.140 19.301 -14.038 0.520 22 B_C25:G6_A B 25 ? A 6 ? 19 1 1 B A 25 1_555 C G 6 1_555 0.035 1.355 -0.639 -9.129 -16.115 -23.306 23 B_A26:G36_C B 26 ? C 36 ? 8 ? 1 B C 26 1_555 C G 5 1_555 0.025 -0.204 -0.017 5.147 -21.043 -2.648 24 B_C27:G35_C B 27 ? C 35 ? 19 1 1 B A 27 1_555 C U 4 1_555 0.252 -0.117 0.436 5.236 -17.112 -2.477 25 B_A28:U34_C B 28 ? C 34 ? 20 1 1 B C 28 1_555 C G 3 1_555 0.058 -0.053 0.007 5.543 -13.407 2.426 26 B_C29:G33_C B 29 ? C 33 ? 19 1 1 B G 29 1_555 C C 2 1_555 -0.300 -0.153 0.138 -7.067 -13.799 -2.979 27 B_G30:C32_C B 30 ? C 32 ? 19 1 1 B A 30 1_555 C U 1 1_555 0.567 -0.149 0.211 -1.092 -8.290 -1.630 28 B_A31:U31_C B 31 ? C 31 ? 20 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 A C 2 1_555 B G 12 1_555 A C 3 1_555 B G 11 1_555 -0.602 -1.650 3.573 -1.842 8.919 32.881 -4.280 0.724 3.062 15.392 3.180 34.086 1 AA_C2C3:G12G13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A C 3 1_555 B G 11 1_555 A C 4 1_555 B G 10 1_555 0.914 -1.648 3.236 1.845 9.825 26.631 -5.418 -1.476 2.535 20.436 -3.838 28.414 2 AA_C3C4:G11G12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A C 4 1_555 B G 10 1_555 A A2M 5 1_555 B A 8 1_555 0.409 -0.601 5.263 -2.071 30.647 72.380 -1.872 -0.420 4.735 24.889 1.682 77.801 3 AA_C4A2M5:A9G11_BB A 4 ? B 11 ? A 5 ? B 9 ? 1 A A2M 5 1_555 B A 8 1_555 A U 7 1_555 B G 7 1_555 -0.895 0.195 3.479 4.102 3.340 7.695 -6.046 14.399 2.546 21.808 -26.790 9.336 4 AA_A2M5U7:G8A9_BB A 5 ? B 9 ? A 7 ? B 8 ? 1 A U 7 1_555 B G 7 1_555 A C 8 1_555 B A 6 1_555 0.231 -0.687 3.197 -2.539 6.089 51.841 -1.169 -0.424 3.090 6.933 2.891 52.230 5 AA_U7C8:A7G8_BB A 7 ? B 8 ? A 8 ? B 7 ? 1 A C 8 1_555 B A 6 1_555 A C 9 1_555 B G 5 1_555 -0.169 -1.368 3.648 -4.557 9.569 39.926 -3.047 -0.286 3.249 13.722 6.535 41.253 6 AA_C8C9:G6A7_BB A 8 ? B 7 ? A 9 ? B 6 ? 1 A C 9 1_555 B G 5 1_555 A A 10 1_555 B U 4 1_555 -0.270 -1.640 3.372 -4.003 12.460 32.260 -4.552 -0.128 2.595 21.360 6.863 34.748 7 AA_C9A10:U5G6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A A 10 1_555 B U 4 1_555 A C 11 1_555 B G 3 1_555 -0.349 -1.420 3.205 -2.368 4.627 31.644 -3.366 0.226 2.990 8.415 4.305 32.057 8 AA_A10C11:G4U5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A C 11 1_555 B G 3 1_555 A C 12 1_555 B G 2 1_555 0.099 -2.016 3.059 1.011 5.627 32.287 -4.430 -0.022 2.681 10.020 -1.800 32.776 9 AA_C11C12:G3G4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A C 12 1_555 B G 2 1_555 A G 13 1_555 B C 1 1_555 0.148 -1.766 3.258 2.059 9.741 29.206 -5.058 0.088 2.555 18.648 -3.942 30.821 10 AA_C12G13:C2G3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 B G 14 1_555 C C 19 1_555 B G 15 1_555 C C 18 1_555 -0.712 -1.168 2.873 -4.671 5.194 34.361 -2.617 0.574 2.743 8.681 7.806 35.043 11 BB_G15G16:C48C49_CC B 15 ? C 49 ? B 16 ? C 48 ? 1 B G 15 1_555 C C 18 1_555 B C 16 1_555 C G 17 1_555 0.208 -1.375 3.329 4.118 9.398 35.082 -3.455 0.220 2.883 15.193 -6.658 36.506 12 BB_G16C17:G47C48_CC B 16 ? C 48 ? B 17 ? C 47 ? 1 B C 16 1_555 C G 17 1_555 B A 17 1_555 C U 16 1_555 0.400 -1.661 3.478 0.308 12.004 30.567 -4.951 -0.657 2.658 21.745 -0.558 32.789 13 BB_C17A18:U46G47_CC B 17 ? C 47 ? B 18 ? C 46 ? 1 B A 17 1_555 C U 16 1_555 B G 18 1_555 C C 15 1_555 0.180 -2.021 3.541 1.035 7.984 29.129 -5.507 -0.135 2.902 15.504 -2.009 30.198 14 BB_A18G19:C45U46_CC B 18 ? C 46 ? B 19 ? C 45 ? 1 B G 18 1_555 C C 15 1_555 B A 19 1_555 C C 14 1_555 0.820 -1.457 3.445 1.521 7.973 38.256 -3.151 -1.040 3.121 12.000 -2.290 39.076 15 BB_G19A20:C44C45_CC B 19 ? C 45 ? B 20 ? C 44 ? 1 B A 19 1_555 C C 14 1_555 B G 20 1_555 C A 13 1_555 -0.611 -0.979 3.125 6.620 5.626 58.258 -1.267 0.940 2.949 5.743 -6.758 58.846 16 BB_A20G21:A43C44_CC B 20 ? C 44 ? B 21 ? C 43 ? 1 B G 20 1_555 C A 13 1_555 B A 21 1_555 C U 11 1_555 -2.249 -0.418 3.464 2.482 0.381 11.813 -2.468 13.831 2.915 1.824 -11.884 12.076 17 BB_G21A22:U41A43_CC B 21 ? C 43 ? B 22 ? C 41 ? 1 B A 21 1_555 C U 11 1_555 B A 22 1_555 C A 10 1_555 -0.095 -2.384 3.502 -9.457 4.269 44.589 -3.456 -0.737 3.227 5.538 12.268 45.720 18 BB_A22A23:A40U41_CC B 22 ? C 41 ? B 23 ? C 40 ? 1 B A 22 1_555 C A 10 1_555 B A 23 1_555 C N6G 8 1_555 -3.249 -3.129 3.585 -3.197 0.896 74.506 -2.614 2.572 3.670 0.740 2.640 74.569 19 BB_A23A24:N6G38A40_CC B 23 ? C 40 ? B 24 ? C 38 ? 1 B A 23 1_555 C N6G 8 1_555 B C 24 1_555 A G 6 1_555 2.592 -0.167 2.891 -1.409 3.986 -31.330 -0.362 4.523 3.000 -7.339 -2.594 -31.607 20 BB_A24C25:G6N6G38_AC B 24 ? C 38 ? B 25 ? A 6 ? 1 B C 24 1_555 A G 6 1_555 B A 25 1_555 C G 6 1_555 0.092 -2.087 3.855 6.741 5.652 46.694 -3.115 0.509 3.573 7.057 -8.417 47.469 21 BB_C25A26:G36G6_CA B 25 ? A 6 ? B 26 ? C 36 ? 1 B A 25 1_555 C G 6 1_555 B C 26 1_555 C G 5 1_555 1.064 -0.699 2.942 -5.091 4.355 29.614 -2.087 -2.911 2.600 8.386 9.802 30.346 22 BB_A26C27:G35G36_CC B 26 ? C 36 ? B 27 ? C 35 ? 1 B C 26 1_555 C G 5 1_555 B A 27 1_555 C U 4 1_555 0.297 -1.210 3.195 -1.803 8.320 37.410 -2.818 -0.663 2.855 12.770 2.767 38.333 23 BB_C27A28:U34G35_CC B 27 ? C 35 ? B 28 ? C 34 ? 1 B A 27 1_555 C U 4 1_555 B C 28 1_555 C G 3 1_555 0.516 -1.126 3.305 4.733 -0.368 31.350 -1.993 -0.051 3.358 -0.676 -8.696 31.699 24 BB_A28C29:G33U34_CC B 28 ? C 34 ? B 29 ? C 33 ? 1 B C 28 1_555 C G 3 1_555 B G 29 1_555 C C 2 1_555 0.110 -1.516 3.398 0.657 11.872 34.476 -4.022 -0.089 2.746 19.332 -1.070 36.410 25 BB_C29G30:C32G33_CC B 29 ? C 33 ? B 30 ? C 32 ? 1 B G 29 1_555 C C 2 1_555 B A 30 1_555 C U 1 1_555 0.751 -1.664 3.019 3.885 3.392 35.091 -3.186 -0.714 2.915 5.589 -6.401 35.456 26 BB_G30A31:U31C32_CC B 30 ? C 32 ? B 31 ? C 31 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'SULFATE ION' SO4 5 'COBALT HEXAMMINE(III)' NCO 6 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 2OUE _pdbx_initial_refinement_model.details ? #