data_3E5F # _entry.id 3E5F # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3E5F pdb_00003e5f 10.2210/pdb3e5f/pdb NDB UR0168 ? ? RCSB RCSB048897 ? ? WWPDB D_1000048897 ? ? # 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 2008-10-07 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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' struct_conn 5 3 'Structure model' struct_conn_type 6 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' '_struct_conn.conn_type_id' 4 3 'Structure model' '_struct_conn.id' 5 3 'Structure model' '_struct_conn.pdbx_dist_value' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 19 3 'Structure model' '_struct_conn_type.id' 20 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 21 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 22 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3E5F _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-08-13 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3e5C 'Same RNA with SAM' unspecified PDB 3e5e 'Same RNA with SAH' unspecified # _audit_author.name 'Lu, C.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 15 _citation.page_first 1076 _citation.page_last 1083 _citation.year 2008 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9993 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18806797 _citation.pdbx_database_id_DOI 10.1038/nsmb.1494 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lu, C.' 1 ? primary 'Smith, A.M.' 2 ? primary 'Fuchs, R.T.' 3 ? primary 'Ding, F.' 4 ? primary 'Rajashankar, K.' 5 ? primary 'Henkin, T.M.' 6 ? primary 'Ke, A.' 7 ? # 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 'SMK box (SAM-III) Riboswitch for RNA' 17402.322 1 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 15 ? ? ? ? 3 non-polymer syn '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium' 446.340 1 ? ? ? ? 4 water nat water 18.015 11 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(GTP)UUCCCGAAAGGAUGGCGGAAACGCCAGAUGCCUUGUAACCGAAAGGGGGAAU' _entity_poly.pdbx_seq_one_letter_code_can GUUCCCGAAAGGAUGGCGGAAACGCCAGAUGCCUUGUAACCGAAAGGGGGAAU _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 3 '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium' EEM 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GTP n 1 2 U n 1 3 U n 1 4 C n 1 5 C n 1 6 C n 1 7 G n 1 8 A n 1 9 A n 1 10 A n 1 11 G n 1 12 G n 1 13 A n 1 14 U n 1 15 G n 1 16 G n 1 17 C n 1 18 G n 1 19 G n 1 20 A n 1 21 A n 1 22 A n 1 23 C n 1 24 G n 1 25 C n 1 26 C n 1 27 A n 1 28 G n 1 29 A n 1 30 U n 1 31 G n 1 32 C n 1 33 C n 1 34 U n 1 35 U n 1 36 G n 1 37 U n 1 38 A n 1 39 A n 1 40 C n 1 41 C n 1 42 G n 1 43 A n 1 44 A n 1 45 A n 1 46 G n 1 47 G n 1 48 G n 1 49 G n 1 50 G n 1 51 A n 1 52 A n 1 53 U n # _pdbx_entity_src_syn.entity_id 1 _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 'The RNA is prepared by in vitro transcription' # 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 EEM non-polymer . '[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium' Se-ADENOSYLSELENOMETHIONINE 'C15 H23 N6 O5 Se 1' 446.340 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 HOH non-polymer . WATER ? 'H2 O' 18.015 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 GTP 1 1 1 GTP GTP A . n A 1 2 U 2 2 2 U U A . n A 1 3 U 3 3 3 U U A . n A 1 4 C 4 4 4 C C A . n A 1 5 C 5 5 5 C C A . n A 1 6 C 6 6 6 C C A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 G 12 12 12 G G A . n A 1 13 A 13 13 13 A A A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 G 16 16 16 G G A . n A 1 17 C 17 17 17 C C A . n A 1 18 G 18 18 18 G G A . n A 1 19 G 19 19 19 G G A . n A 1 20 A 20 20 20 A A A . n A 1 21 A 21 21 21 A A A . n A 1 22 A 22 22 22 A A A . n A 1 23 C 23 23 23 C C A . n A 1 24 G 24 24 24 G G A . n A 1 25 C 25 25 25 C C A . n A 1 26 C 26 26 26 C C A . n A 1 27 A 27 27 27 A A A . n A 1 28 G 28 28 28 G G A . n A 1 29 A 29 29 29 A A A . n A 1 30 U 30 30 30 U U A . n A 1 31 G 31 31 31 G G A . n A 1 32 C 32 32 32 C C A . n A 1 33 C 33 33 33 C C A . n A 1 34 U 34 34 34 U U A . n A 1 35 U 35 35 35 U U A . n A 1 36 G 36 36 36 G G A . n A 1 37 U 37 37 37 U U A . n A 1 38 A 38 38 38 A A A . n A 1 39 A 39 39 39 A A A . n A 1 40 C 40 40 40 C C A . n A 1 41 C 41 41 41 C C A . n A 1 42 G 42 42 42 G G A . n A 1 43 A 43 43 43 A A A . n A 1 44 A 44 44 44 A A A . n A 1 45 A 45 45 45 A A A . n A 1 46 G 46 46 46 G G A . n A 1 47 G 47 47 47 G G A . n A 1 48 G 48 48 48 G G A . n A 1 49 G 49 49 49 G G A . n A 1 50 G 50 50 50 G G A . n A 1 51 A 51 51 51 A A A . n A 1 52 A 52 52 52 A A A . n A 1 53 U 53 53 53 U U A . 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 B 2 SR 1 201 201 SR SR A . C 2 SR 1 202 202 SR SR A . D 2 SR 1 203 203 SR SR A . E 2 SR 1 204 204 SR SR A . F 2 SR 1 205 205 SR SR A . G 2 SR 1 206 206 SR SR A . H 2 SR 1 207 207 SR SR A . I 2 SR 1 208 208 SR SR A . J 2 SR 1 209 209 SR SR A . K 2 SR 1 210 210 SR SR A . L 2 SR 1 211 211 SR SR A . M 2 SR 1 212 212 SR SR A . N 2 SR 1 213 213 SR SR A . O 2 SR 1 214 214 SR SR A . P 2 SR 1 215 215 SR SR A . Q 3 EEM 1 216 216 EEM EEM A . R 4 HOH 1 217 217 HOH HOH A . R 4 HOH 2 218 218 HOH HOH A . R 4 HOH 3 219 219 HOH HOH A . R 4 HOH 4 220 220 HOH HOH A . R 4 HOH 5 221 221 HOH HOH A . R 4 HOH 6 222 222 HOH HOH A . R 4 HOH 7 223 223 HOH HOH A . R 4 HOH 8 224 224 HOH HOH A . R 4 HOH 9 225 225 HOH HOH A . R 4 HOH 10 226 226 HOH HOH A . R 4 HOH 11 227 227 HOH HOH A . # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal CNS 1.2 ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns-online.org/ Fortran_77 ? 1 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 2 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 3 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 4 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? 5 PHASER . ? ? ? ? phasing ? ? ? 6 # _cell.entry_id 3E5F _cell.length_a 96.776 _cell.length_b 96.776 _cell.length_c 86.765 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _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 3E5F _symmetry.space_group_name_H-M 'I 41 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3E5F _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.92 _exptl_crystal.density_percent_sol 57.85 _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 7 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '40 mM sodium cacodylate, 80 mM SrCl, 15% MPD, 2 mM spermine-HCl, pH 7, vapor diffusion, hanging drop, temperature 298K' # 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 'sodium cacodylate' ? ? ? 1 2 1 MPD ? ? ? 1 3 1 spermine-HCl ? ? ? 1 4 2 'sodium cacodylate' ? ? ? 1 5 2 MPD ? ? ? # _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 2008-03-02 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9792 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 24-ID-E' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 24-ID-E _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9792 # _reflns.entry_id 3E5F _reflns.observed_criterion_sigma_I 9.3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 2.7 _reflns.number_obs 5520 _reflns.number_all ? _reflns.percent_possible_obs 93.7 _reflns.pdbx_Rmerge_I_obs 0.076 _reflns.pdbx_Rsym_value 0.076 _reflns.pdbx_netI_over_sigmaI 13.3 _reflns.B_iso_Wilson_estimate 71.1 _reflns.pdbx_redundancy 3.9 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.7 _reflns_shell.d_res_low 2.8 _reflns_shell.percent_possible_all 74 _reflns_shell.Rmerge_I_obs 0.236 _reflns_shell.pdbx_Rsym_value 0.284 _reflns_shell.meanI_over_sigI_obs 1.7 _reflns_shell.pdbx_redundancy 2.8 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3E5F _refine.ls_number_reflns_obs 5519 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 1444146.87 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.79 _refine.ls_d_res_high 2.70 _refine.ls_percent_reflns_obs 93.6 _refine.ls_R_factor_obs 0.227 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.227 _refine.ls_R_factor_R_free 0.255 _refine.ls_R_factor_R_free_error 0.011 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.7 _refine.ls_number_reflns_R_free 538 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 0.50 _refine.occupancy_max 1.00 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 57.1 _refine.aniso_B[1][1] -8.04 _refine.aniso_B[2][2] -8.04 _refine.aniso_B[3][3] 16.08 _refine.aniso_B[1][2] 0.00 _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 0.4 _refine.solvent_model_param_bsol 56.7708 _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 'BULK SOLVENT MODEL USED, REFMAC WAS ALSO USED FOR REFINEMENT' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _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.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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_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 3E5F _refine_analyze.Luzzati_coordinate_error_obs 0.32 _refine_analyze.Luzzati_sigma_a_obs 0.41 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.38 _refine_analyze.Luzzati_sigma_a_free 0.36 _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 1155 _refine_hist.pdbx_number_atoms_ligand 42 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 1208 _refine_hist.d_res_high 2.70 _refine_hist.d_res_low 19.79 # 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 0.005 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.3 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 17.0 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.49 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.70 _refine_ls_shell.d_res_low 2.87 _refine_ls_shell.number_reflns_R_work 648 _refine_ls_shell.R_factor_R_work 0.326 _refine_ls_shell.percent_reflns_obs 75.8 _refine_ls_shell.R_factor_R_free 0.329 _refine_ls_shell.R_factor_R_free_error 0.038 _refine_ls_shell.percent_reflns_R_free 10.2 _refine_ls_shell.number_reflns_R_free 74 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 ion.param ion.top 'X-RAY DIFFRACTION' 2 water_rep.param dna-rna.top 'X-RAY DIFFRACTION' 3 dna-rna_rep.param water.top 'X-RAY DIFFRACTION' 4 gtp.param gtp.top 'X-RAY DIFFRACTION' 5 sesam.param sesam.top 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3E5F _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 3E5F _struct.title 'Crystal Structures of the SMK box (SAM-III) Riboswitch with Se-SAM' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3E5F _struct_keywords.text 'SMK SAM riboswitch Shine-Delgarno translation regulation, RNA' _struct_keywords.pdbx_keywords 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 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 2 ? L N N 2 ? M N N 2 ? N N N 2 ? O N N 2 ? P N N 2 ? Q N N 3 ? R N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3E5F _struct_ref.pdbx_db_accession 3E5F _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GUUCCCGAAAGGAUGGCGGAAACGCCAGAUGCCUUGUAACCGAAAGGGGGAAU _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3E5F _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 53 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3E5F _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 53 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 53 # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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,J,K,L,M,N,O,P,Q,R # _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 # _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 GTP 1 "O3'" ? ? ? 1_555 A U 2 P ? ? A GTP 1 A U 2 1_555 ? ? ? ? ? ? ? 1.691 ? ? metalc1 metalc ? ? A C 6 OP2 ? ? ? 1_555 H SR . SR ? ? A C 6 A SR 207 1_555 ? ? ? ? ? ? ? 2.630 ? ? metalc2 metalc ? ? A U 14 O4 ? ? ? 1_555 N SR . SR ? ? A U 14 A SR 213 1_555 ? ? ? ? ? ? ? 2.760 ? ? metalc3 metalc ? ? A U 34 OP2 ? ? ? 1_555 I SR . SR ? ? A U 34 A SR 208 1_555 ? ? ? ? ? ? ? 2.777 ? ? metalc4 metalc ? ? A A 38 OP2 ? ? ? 1_555 P SR . SR ? ? A A 38 A SR 215 1_555 ? ? ? ? ? ? ? 2.681 ? ? metalc5 metalc ? ? I SR . SR ? ? ? 1_555 R HOH . O ? ? A SR 208 A HOH 217 1_555 ? ? ? ? ? ? ? 2.760 ? ? metalc6 metalc ? ? N SR . SR ? ? ? 1_555 R HOH . O ? ? A SR 213 A HOH 223 1_555 ? ? ? ? ? ? ? 2.732 ? ? hydrog1 hydrog ? ? A GTP 1 N1 ? ? ? 1_555 A U 53 O2 ? ? A GTP 1 A U 53 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A GTP 1 O6 ? ? ? 1_555 A U 53 N3 ? ? A GTP 1 A U 53 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A U 2 N3 ? ? ? 1_555 A A 52 N1 ? ? A U 2 A A 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 O4 ? ? ? 1_555 A A 52 N6 ? ? A U 2 A A 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 51 N1 ? ? A U 3 A A 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 51 N6 ? ? A U 3 A A 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 50 N1 ? ? A C 4 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 50 O6 ? ? A C 4 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 50 N2 ? ? A C 4 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 49 N1 ? ? A C 5 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 49 O6 ? ? A C 5 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 49 N2 ? ? A C 5 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 48 N1 ? ? A C 6 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 48 O6 ? ? A C 6 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 48 N2 ? ? A C 6 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 8 N6 ? ? ? 1_555 A G 36 N3 ? ? A A 8 A G 36 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A A 8 N7 ? ? ? 1_555 A G 36 N2 ? ? A A 8 A G 36 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A A 9 N1 ? ? ? 1_555 A U 35 N3 ? ? A A 9 A U 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 9 N6 ? ? ? 1_555 A U 35 O4 ? ? A A 9 A U 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 34 N3 ? ? A A 10 A U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 34 O4 ? ? A A 10 A U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 33 N3 ? ? A G 11 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 33 O2 ? ? A G 11 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 33 N4 ? ? A G 11 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 32 N3 ? ? A G 12 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 32 O2 ? ? A G 12 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 32 N4 ? ? A G 12 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 13 N1 ? ? ? 1_555 A G 28 N1 ? ? A A 13 A G 28 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog29 hydrog ? ? A A 13 N6 ? ? ? 1_555 A G 28 O6 ? ? A A 13 A G 28 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog30 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 27 N1 ? ? A U 14 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 27 N6 ? ? A U 14 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 15 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 15 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 15 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 15 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 15 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 15 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 16 N1 ? ? ? 1_555 A C 25 N3 ? ? A G 16 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 16 N2 ? ? ? 1_555 A C 25 O2 ? ? A G 16 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 16 O6 ? ? ? 1_555 A C 25 N4 ? ? A G 16 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 17 N3 ? ? ? 1_555 A G 24 N1 ? ? A C 17 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 17 N4 ? ? ? 1_555 A G 24 O6 ? ? A C 17 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 17 O2 ? ? ? 1_555 A G 24 N2 ? ? A C 17 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 18 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 18 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 18 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 19 N2 ? ? ? 1_555 A A 22 N7 ? ? A G 19 A A 22 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog45 hydrog ? ? A G 19 N3 ? ? ? 1_555 A A 22 N6 ? ? A G 19 A A 22 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog46 hydrog ? ? A G 31 N7 ? ? ? 1_555 A G 36 N1 ? ? A G 31 A G 36 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog47 hydrog ? ? A G 31 O6 ? ? ? 1_555 A G 36 N2 ? ? A G 31 A G 36 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog48 hydrog ? ? A A 38 N1 ? ? ? 1_555 A G 48 N2 ? ? A A 38 A G 48 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog49 hydrog ? ? A A 38 N6 ? ? ? 1_555 A G 48 N3 ? ? A A 38 A G 48 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog50 hydrog ? ? A C 40 N3 ? ? ? 1_555 A G 47 N1 ? ? A C 40 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 40 N4 ? ? ? 1_555 A G 47 O6 ? ? A C 40 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 40 O2 ? ? ? 1_555 A G 47 N2 ? ? A C 40 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A C 41 N3 ? ? ? 1_555 A G 46 N1 ? ? A C 41 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A C 41 N4 ? ? ? 1_555 A G 46 O6 ? ? A C 41 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A C 41 O2 ? ? ? 1_555 A G 46 N2 ? ? A C 41 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A G 42 N2 ? ? ? 1_555 A A 45 N7 ? ? A G 42 A A 45 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # 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 O4 ? A U 14 ? A U 14 ? 1_555 SR ? N SR . ? A SR 213 ? 1_555 O ? R HOH . ? A HOH 223 ? 1_555 102.6 ? 2 OP2 ? A U 34 ? A U 34 ? 1_555 SR ? I SR . ? A SR 208 ? 1_555 O ? R HOH . ? A HOH 217 ? 1_555 94.3 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SR 204 ? 1 'BINDING SITE FOR RESIDUE SR A 204' AC2 Software A SR 206 ? 2 'BINDING SITE FOR RESIDUE SR A 206' AC3 Software A SR 207 ? 2 'BINDING SITE FOR RESIDUE SR A 207' AC4 Software A SR 208 ? 3 'BINDING SITE FOR RESIDUE SR A 208' AC5 Software A SR 209 ? 1 'BINDING SITE FOR RESIDUE SR A 209' AC6 Software A SR 211 ? 1 'BINDING SITE FOR RESIDUE SR A 211' AC7 Software A SR 212 ? 1 'BINDING SITE FOR RESIDUE SR A 212' AC8 Software A SR 213 ? 3 'BINDING SITE FOR RESIDUE SR A 213' AC9 Software A SR 215 ? 2 'BINDING SITE FOR RESIDUE SR A 215' BC1 Software A EEM 216 ? 8 'BINDING SITE FOR RESIDUE EEM A 216' # 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 1 G A 46 ? G A 46 . ? 1_555 ? 2 AC2 2 G A 19 ? G A 19 . ? 1_555 ? 3 AC2 2 A A 21 ? A A 21 . ? 1_555 ? 4 AC3 2 C A 6 ? C A 6 . ? 1_555 ? 5 AC3 2 HOH R . ? HOH A 219 . ? 1_555 ? 6 AC4 3 U A 34 ? U A 34 . ? 1_555 ? 7 AC4 3 G A 36 ? G A 36 . ? 1_555 ? 8 AC4 3 HOH R . ? HOH A 217 . ? 1_555 ? 9 AC5 1 A A 38 ? A A 38 . ? 1_555 ? 10 AC6 1 G A 19 ? G A 19 . ? 1_555 ? 11 AC7 1 GTP A 1 ? GTP A 1 . ? 1_555 ? 12 AC8 3 U A 14 ? U A 14 . ? 1_555 ? 13 AC8 3 G A 15 ? G A 15 . ? 1_555 ? 14 AC8 3 HOH R . ? HOH A 223 . ? 1_555 ? 15 AC9 2 A A 38 ? A A 38 . ? 1_555 ? 16 AC9 2 A A 39 ? A A 39 . ? 1_555 ? 17 BC1 8 G A 7 ? G A 7 . ? 1_555 ? 18 BC1 8 U A 30 ? U A 30 . ? 1_555 ? 19 BC1 8 G A 31 ? G A 31 . ? 1_555 ? 20 BC1 8 G A 36 ? G A 36 . ? 1_555 ? 21 BC1 8 U A 37 ? U A 37 . ? 1_555 ? 22 BC1 8 A A 38 ? A A 38 . ? 1_555 ? 23 BC1 8 G A 47 ? G A 47 . ? 1_555 ? 24 BC1 8 G A 48 ? G A 48 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OP2 A G 12 ? ? O A HOH 225 ? ? 2.19 2 1 "O2'" A U 53 ? ? O A HOH 220 ? ? 2.19 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 GTP _pdbx_validate_rmsd_bond.auth_seq_id_1 1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 P _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 U _pdbx_validate_rmsd_bond.auth_seq_id_2 2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.691 _pdbx_validate_rmsd_bond.bond_target_value 1.607 _pdbx_validate_rmsd_bond.bond_deviation 0.084 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.012 _pdbx_validate_rmsd_bond.linker_flag Y # 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 "O3'" A GTP 1 ? ? P A U 2 ? ? "O5'" A U 2 ? ? 89.25 104.00 -14.75 1.90 Y 2 1 "O3'" A GTP 1 ? ? P A U 2 ? ? OP2 A U 2 ? ? 120.37 110.50 9.87 1.10 Y # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id GTP _pdbx_struct_mod_residue.label_seq_id 1 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id GTP _pdbx_struct_mod_residue.auth_seq_id 1 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id G _pdbx_struct_mod_residue.details "GUANOSINE-5'-TRIPHOSPHATE" # 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 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 EEM C2 C Y N 73 EEM N3 N Y N 74 EEM C4 C Y N 75 EEM "C1'" C N R 76 EEM "C2'" C N R 77 EEM "C3'" C N S 78 EEM "C4'" C N S 79 EEM "C5'" C N N 80 EEM O O N N 81 EEM C C N N 82 EEM OXT O N N 83 EEM CA C N S 84 EEM N N N N 85 EEM CB C N N 86 EEM CG C N N 87 EEM SE SE N S 88 EEM CE C N N 89 EEM "O4'" O N N 90 EEM "O3'" O N N 91 EEM "O2'" O N N 92 EEM N9 N Y N 93 EEM C8 C Y N 94 EEM N7 N Y N 95 EEM C5 C Y N 96 EEM N1 N Y N 97 EEM C6 C Y N 98 EEM N6 N N N 99 EEM H2 H N N 100 EEM "H1'" H N N 101 EEM "H2'" H N N 102 EEM "H3'" H N N 103 EEM "H4'" H N N 104 EEM "H5'" H N N 105 EEM "H5'A" H N N 106 EEM HOXT H N N 107 EEM HA H N N 108 EEM HN H N N 109 EEM HNA H N N 110 EEM HB H N N 111 EEM HBA H N N 112 EEM HG H N N 113 EEM HGA H N N 114 EEM HE H N N 115 EEM HEA H N N 116 EEM HEB H N N 117 EEM "HO3'" H N N 118 EEM "HO2'" H N N 119 EEM H8 H N N 120 EEM HN6 H N N 121 EEM HN6A H N N 122 G OP3 O N N 123 G P P N N 124 G OP1 O N N 125 G OP2 O N N 126 G "O5'" O N N 127 G "C5'" C N N 128 G "C4'" C N R 129 G "O4'" O N N 130 G "C3'" C N S 131 G "O3'" O N N 132 G "C2'" C N R 133 G "O2'" O N N 134 G "C1'" C N R 135 G N9 N Y N 136 G C8 C Y N 137 G N7 N Y N 138 G C5 C Y N 139 G C6 C N N 140 G O6 O N N 141 G N1 N N N 142 G C2 C N N 143 G N2 N N N 144 G N3 N N N 145 G C4 C Y N 146 G HOP3 H N N 147 G HOP2 H N N 148 G "H5'" H N N 149 G "H5''" H N N 150 G "H4'" H N N 151 G "H3'" H N N 152 G "HO3'" H N N 153 G "H2'" H N N 154 G "HO2'" H N N 155 G "H1'" H N N 156 G H8 H N N 157 G H1 H N N 158 G H21 H N N 159 G H22 H N N 160 GTP PG P N N 161 GTP O1G O N N 162 GTP O2G O N N 163 GTP O3G O N N 164 GTP O3B O N N 165 GTP PB P N N 166 GTP O1B O N N 167 GTP O2B O N N 168 GTP O3A O N N 169 GTP PA P N N 170 GTP O1A O N N 171 GTP O2A O N N 172 GTP "O5'" O N N 173 GTP "C5'" C N N 174 GTP "C4'" C N R 175 GTP "O4'" O N N 176 GTP "C3'" C N S 177 GTP "O3'" O N N 178 GTP "C2'" C N R 179 GTP "O2'" O N N 180 GTP "C1'" C N R 181 GTP N9 N Y N 182 GTP C8 C Y N 183 GTP N7 N Y N 184 GTP C5 C Y N 185 GTP C6 C N N 186 GTP O6 O N N 187 GTP N1 N N N 188 GTP C2 C N N 189 GTP N2 N N N 190 GTP N3 N N N 191 GTP C4 C Y N 192 GTP HOG2 H N N 193 GTP HOG3 H N N 194 GTP HOB2 H N N 195 GTP HOA2 H N N 196 GTP "H5'" H N N 197 GTP "H5''" H N N 198 GTP "H4'" H N N 199 GTP "H3'" H N N 200 GTP "HO3'" H N N 201 GTP "H2'" H N N 202 GTP "HO2'" H N N 203 GTP "H1'" H N N 204 GTP H8 H N N 205 GTP HN1 H N N 206 GTP HN21 H N N 207 GTP HN22 H N N 208 HOH O O N N 209 HOH H1 H N N 210 HOH H2 H N N 211 SR SR SR N N 212 U OP3 O N N 213 U P P N N 214 U OP1 O N N 215 U OP2 O N N 216 U "O5'" O N N 217 U "C5'" C N N 218 U "C4'" C N R 219 U "O4'" O N N 220 U "C3'" C N S 221 U "O3'" O N N 222 U "C2'" C N R 223 U "O2'" O N N 224 U "C1'" C N R 225 U N1 N N N 226 U C2 C N N 227 U O2 O N N 228 U N3 N N N 229 U C4 C N N 230 U O4 O N N 231 U C5 C N N 232 U C6 C N N 233 U HOP3 H N N 234 U HOP2 H N N 235 U "H5'" H N N 236 U "H5''" H N N 237 U "H4'" H N N 238 U "H3'" H N N 239 U "HO3'" H N N 240 U "H2'" H N N 241 U "HO2'" H N N 242 U "H1'" H N N 243 U H3 H N N 244 U H5 H N N 245 U H6 H N N 246 # 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 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 EEM N1 C2 doub Y N 76 EEM C2 N3 sing Y N 77 EEM C2 H2 sing N N 78 EEM C4 N3 doub Y N 79 EEM C5 C4 sing Y N 80 EEM N9 C4 sing Y N 81 EEM N9 "C1'" sing N N 82 EEM "C1'" "O4'" sing N N 83 EEM "C1'" "C2'" sing N N 84 EEM "C1'" "H1'" sing N N 85 EEM "O2'" "C2'" sing N N 86 EEM "C2'" "C3'" sing N N 87 EEM "C2'" "H2'" sing N N 88 EEM "C4'" "C3'" sing N N 89 EEM "O3'" "C3'" sing N N 90 EEM "C3'" "H3'" sing N N 91 EEM "O4'" "C4'" sing N N 92 EEM "C4'" "C5'" sing N N 93 EEM "C4'" "H4'" sing N N 94 EEM "C5'" "H5'" sing N N 95 EEM "C5'" "H5'A" sing N N 96 EEM "C5'" SE sing N N 97 EEM C O doub N N 98 EEM CA C sing N N 99 EEM C OXT sing N N 100 EEM OXT HOXT sing N N 101 EEM CB CA sing N N 102 EEM N CA sing N N 103 EEM CA HA sing N N 104 EEM N HN sing N N 105 EEM N HNA sing N N 106 EEM CB CG sing N N 107 EEM CB HB sing N N 108 EEM CB HBA sing N N 109 EEM SE CG sing N N 110 EEM CG HG sing N N 111 EEM CG HGA sing N N 112 EEM SE CE sing N N 113 EEM CE HE sing N N 114 EEM CE HEA sing N N 115 EEM CE HEB sing N N 116 EEM "O3'" "HO3'" sing N N 117 EEM "O2'" "HO2'" sing N N 118 EEM C8 N9 sing Y N 119 EEM N7 C8 doub Y N 120 EEM C8 H8 sing N N 121 EEM N7 C5 sing Y N 122 EEM C6 C5 doub Y N 123 EEM C6 N1 sing Y N 124 EEM N6 C6 sing N N 125 EEM N6 HN6 sing N N 126 EEM N6 HN6A sing N N 127 G OP3 P sing N N 128 G OP3 HOP3 sing N N 129 G P OP1 doub N N 130 G P OP2 sing N N 131 G P "O5'" sing N N 132 G OP2 HOP2 sing N N 133 G "O5'" "C5'" sing N N 134 G "C5'" "C4'" sing N N 135 G "C5'" "H5'" sing N N 136 G "C5'" "H5''" sing N N 137 G "C4'" "O4'" sing N N 138 G "C4'" "C3'" sing N N 139 G "C4'" "H4'" sing N N 140 G "O4'" "C1'" sing N N 141 G "C3'" "O3'" sing N N 142 G "C3'" "C2'" sing N N 143 G "C3'" "H3'" sing N N 144 G "O3'" "HO3'" sing N N 145 G "C2'" "O2'" sing N N 146 G "C2'" "C1'" sing N N 147 G "C2'" "H2'" sing N N 148 G "O2'" "HO2'" sing N N 149 G "C1'" N9 sing N N 150 G "C1'" "H1'" sing N N 151 G N9 C8 sing Y N 152 G N9 C4 sing Y N 153 G C8 N7 doub Y N 154 G C8 H8 sing N N 155 G N7 C5 sing Y N 156 G C5 C6 sing N N 157 G C5 C4 doub Y N 158 G C6 O6 doub N N 159 G C6 N1 sing N N 160 G N1 C2 sing N N 161 G N1 H1 sing N N 162 G C2 N2 sing N N 163 G C2 N3 doub N N 164 G N2 H21 sing N N 165 G N2 H22 sing N N 166 G N3 C4 sing N N 167 GTP PG O1G doub N N 168 GTP PG O2G sing N N 169 GTP PG O3G sing N N 170 GTP PG O3B sing N N 171 GTP O2G HOG2 sing N N 172 GTP O3G HOG3 sing N N 173 GTP O3B PB sing N N 174 GTP PB O1B doub N N 175 GTP PB O2B sing N N 176 GTP PB O3A sing N N 177 GTP O2B HOB2 sing N N 178 GTP O3A PA sing N N 179 GTP PA O1A doub N N 180 GTP PA O2A sing N N 181 GTP PA "O5'" sing N N 182 GTP O2A HOA2 sing N N 183 GTP "O5'" "C5'" sing N N 184 GTP "C5'" "C4'" sing N N 185 GTP "C5'" "H5'" sing N N 186 GTP "C5'" "H5''" sing N N 187 GTP "C4'" "O4'" sing N N 188 GTP "C4'" "C3'" sing N N 189 GTP "C4'" "H4'" sing N N 190 GTP "O4'" "C1'" sing N N 191 GTP "C3'" "O3'" sing N N 192 GTP "C3'" "C2'" sing N N 193 GTP "C3'" "H3'" sing N N 194 GTP "O3'" "HO3'" sing N N 195 GTP "C2'" "O2'" sing N N 196 GTP "C2'" "C1'" sing N N 197 GTP "C2'" "H2'" sing N N 198 GTP "O2'" "HO2'" sing N N 199 GTP "C1'" N9 sing N N 200 GTP "C1'" "H1'" sing N N 201 GTP N9 C8 sing Y N 202 GTP N9 C4 sing Y N 203 GTP C8 N7 doub Y N 204 GTP C8 H8 sing N N 205 GTP N7 C5 sing Y N 206 GTP C5 C6 sing N N 207 GTP C5 C4 doub Y N 208 GTP C6 O6 doub N N 209 GTP C6 N1 sing N N 210 GTP N1 C2 sing N N 211 GTP N1 HN1 sing N N 212 GTP C2 N2 sing N N 213 GTP C2 N3 doub N N 214 GTP N2 HN21 sing N N 215 GTP N2 HN22 sing N N 216 GTP N3 C4 sing N N 217 HOH O H1 sing N N 218 HOH O H2 sing N N 219 U OP3 P sing N N 220 U OP3 HOP3 sing N N 221 U P OP1 doub N N 222 U P OP2 sing N N 223 U P "O5'" sing N N 224 U OP2 HOP2 sing N N 225 U "O5'" "C5'" sing N N 226 U "C5'" "C4'" sing N N 227 U "C5'" "H5'" sing N N 228 U "C5'" "H5''" sing N N 229 U "C4'" "O4'" sing N N 230 U "C4'" "C3'" sing N N 231 U "C4'" "H4'" sing N N 232 U "O4'" "C1'" sing N N 233 U "C3'" "O3'" sing N N 234 U "C3'" "C2'" sing N N 235 U "C3'" "H3'" sing N N 236 U "O3'" "HO3'" sing N N 237 U "C2'" "O2'" sing N N 238 U "C2'" "C1'" sing N N 239 U "C2'" "H2'" sing N N 240 U "O2'" "HO2'" sing N N 241 U "C1'" N1 sing N N 242 U "C1'" "H1'" sing N N 243 U N1 C2 sing N N 244 U N1 C6 sing N N 245 U C2 O2 doub N N 246 U C2 N3 sing N N 247 U N3 C4 sing N N 248 U N3 H3 sing N N 249 U C4 O4 doub N N 250 U C4 C5 sing N N 251 U C5 C6 doub N N 252 U C5 H5 sing N N 253 U C6 H6 sing N N 254 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3E5F 'double helix' 3E5F 'a-form double helix' 3E5F tetraloop 3E5F 'bulge loop' 3E5F 'mismatched base pair' 3E5F 'three-way junction' # 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 GTP 1 1_555 A U 53 1_555 -2.211 -0.779 0.197 -1.219 -12.574 -6.190 1 A_GTP1:U53_A A 1 ? A 53 ? 28 ? 1 A U 2 1_555 A A 52 1_555 -0.128 -0.257 0.112 5.302 -18.246 4.251 2 A_U2:A52_A A 2 ? A 52 ? 20 1 1 A U 3 1_555 A A 51 1_555 -0.090 -0.130 -0.007 8.813 -12.186 6.042 3 A_U3:A51_A A 3 ? A 51 ? 20 1 1 A C 4 1_555 A G 50 1_555 0.300 -0.191 0.080 8.730 -14.473 2.449 4 A_C4:G50_A A 4 ? A 50 ? 19 1 1 A C 5 1_555 A G 49 1_555 0.197 -0.101 -0.055 5.832 -0.106 2.358 5 A_C5:G49_A A 5 ? A 49 ? 19 1 1 A C 6 1_555 A G 48 1_555 0.390 -0.256 -0.374 15.277 -5.929 1.202 6 A_C6:G48_A A 6 ? A 48 ? 19 1 1 A A 22 1_555 A G 19 1_555 -6.662 -4.622 0.657 -15.351 3.751 -13.763 7 A_A22:G19_A A 22 ? A 19 ? 11 10 1 A C 23 1_555 A G 18 1_555 0.189 -0.179 0.049 0.881 1.909 -1.026 8 A_C23:G18_A A 23 ? A 18 ? 19 1 1 A G 24 1_555 A C 17 1_555 -0.568 -0.255 -0.039 1.293 -8.799 0.598 9 A_G24:C17_A A 24 ? A 17 ? 19 1 1 A C 25 1_555 A G 16 1_555 0.896 -0.173 -0.015 5.142 -9.794 8.987 10 A_C25:G16_A A 25 ? A 16 ? 19 1 1 A C 26 1_555 A G 15 1_555 0.582 -0.213 0.385 -4.179 -10.754 8.637 11 A_C26:G15_A A 26 ? A 15 ? 19 1 1 A A 27 1_555 A U 14 1_555 -0.942 -0.114 0.918 -7.654 -13.332 1.487 12 A_A27:U14_A A 27 ? A 14 ? 20 1 1 A G 28 1_555 A A 13 1_555 0.180 1.609 0.361 8.726 -18.680 -12.127 13 A_G28:A13_A A 28 ? A 13 ? 8 1 1 A C 32 1_555 A G 12 1_555 -0.007 -0.039 0.272 -3.768 -5.035 5.070 14 A_C32:G12_A A 32 ? A 12 ? 19 1 1 A C 33 1_555 A G 11 1_555 0.016 -0.187 -0.159 -3.750 -4.287 2.743 15 A_C33:G11_A A 33 ? A 11 ? 19 1 1 A U 34 1_555 A A 10 1_555 -0.001 -0.021 -0.060 2.676 0.577 0.217 16 A_U34:A10_A A 34 ? A 10 ? 20 1 1 A U 35 1_555 A A 9 1_555 -0.087 -0.044 -0.356 10.926 -0.999 10.606 17 A_U35:A9_A A 35 ? A 9 ? 20 1 1 A G 36 1_555 A G 31 1_555 5.118 -0.096 0.216 23.512 12.756 -115.799 18 A_G36:G31_A A 36 ? A 31 ? 7 ? 1 A C 40 1_555 A G 47 1_555 0.493 -0.284 -0.166 3.916 -12.245 1.580 19 A_C40:G47_A A 40 ? A 47 ? 19 1 1 A C 41 1_555 A G 46 1_555 0.515 -0.338 -0.033 0.577 -0.501 -2.062 20 A_C41:G46_A A 41 ? A 46 ? 19 1 1 A G 42 1_555 A A 45 1_555 7.891 -5.076 0.943 12.281 -12.004 -45.367 21 A_G42:A45_A A 42 ? A 45 ? ? ? # 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 GTP 1 1_555 A U 53 1_555 A U 2 1_555 A A 52 1_555 0.244 -0.899 3.087 -2.623 9.176 42.996 -1.993 -0.552 2.828 12.338 3.527 43.993 1 AA_GTP1U2:A52U53_AA A 1 ? A 53 ? A 2 ? A 52 ? 1 A U 2 1_555 A A 52 1_555 A U 3 1_555 A A 51 1_555 -0.045 -0.969 3.099 -2.926 7.215 32.578 -2.775 -0.365 2.819 12.638 5.125 33.471 2 AA_U2U3:A51A52_AA A 2 ? A 52 ? A 3 ? A 51 ? 1 A U 3 1_555 A A 51 1_555 A C 4 1_555 A G 50 1_555 0.069 -1.571 3.296 -0.789 -0.747 35.521 -2.463 -0.230 3.325 -1.224 1.292 35.537 3 AA_U3C4:G50A51_AA A 3 ? A 51 ? A 4 ? A 50 ? 1 A C 4 1_555 A G 50 1_555 A C 5 1_555 A G 49 1_555 -0.570 -2.078 3.282 -2.564 8.881 27.432 -5.961 0.622 2.540 18.088 5.223 28.919 4 AA_C4C5:G49G50_AA A 4 ? A 50 ? A 5 ? A 49 ? 1 A C 5 1_555 A G 49 1_555 A C 6 1_555 A G 48 1_555 -0.358 -1.797 3.115 -0.316 5.050 28.089 -4.689 0.662 2.760 10.299 0.645 28.532 5 AA_C5C6:G48G49_AA A 5 ? A 49 ? A 6 ? A 48 ? 1 A A 22 1_555 A G 19 1_555 A C 23 1_555 A G 18 1_555 1.833 -0.998 2.837 3.162 3.603 49.317 -1.423 -1.984 2.867 4.306 -3.779 49.535 6 AA_A22C23:G18G19_AA A 22 ? A 19 ? A 23 ? A 18 ? 1 A C 23 1_555 A G 18 1_555 A G 24 1_555 A C 17 1_555 -0.764 -2.076 3.162 -0.508 5.713 24.316 -6.328 1.632 2.628 13.327 1.186 24.974 7 AA_C23G24:C17G18_AA A 23 ? A 18 ? A 24 ? A 17 ? 1 A G 24 1_555 A C 17 1_555 A C 25 1_555 A G 16 1_555 0.807 -1.664 3.179 -0.912 1.646 36.105 -2.904 -1.423 3.082 2.653 1.470 36.153 8 AA_G24C25:G16C17_AA A 24 ? A 17 ? A 25 ? A 16 ? 1 A C 25 1_555 A G 16 1_555 A C 26 1_555 A G 15 1_555 0.422 -1.988 3.154 0.596 10.660 30.299 -5.256 -0.671 2.346 19.644 -1.098 32.084 9 AA_C25C26:G15G16_AA A 25 ? A 16 ? A 26 ? A 15 ? 1 A C 26 1_555 A G 15 1_555 A A 27 1_555 A U 14 1_555 -0.377 -1.967 2.719 -2.706 19.069 29.619 -5.150 0.354 1.285 33.245 4.717 35.212 10 AA_C26A27:U14G15_AA A 26 ? A 15 ? A 27 ? A 14 ? 1 A A 27 1_555 A U 14 1_555 A G 28 1_555 A A 13 1_555 -1.113 -0.694 2.948 5.731 4.278 33.561 -1.755 2.663 2.622 7.306 -9.788 34.293 11 AA_A27G28:A13U14_AA A 27 ? A 14 ? A 28 ? A 13 ? 1 A G 28 1_555 A A 13 1_555 A C 32 1_555 A G 12 1_555 -1.423 -2.509 2.892 -7.388 13.869 50.893 -3.535 1.203 2.353 15.715 8.371 53.109 12 AA_G28C32:G12A13_AA A 28 ? A 13 ? A 32 ? A 12 ? 1 A C 32 1_555 A G 12 1_555 A C 33 1_555 A G 11 1_555 -0.991 -2.341 2.916 0.299 6.819 30.544 -5.391 1.884 2.342 12.745 -0.558 31.280 13 AA_C32C33:G11G12_AA A 32 ? A 12 ? A 33 ? A 11 ? 1 A C 33 1_555 A G 11 1_555 A U 34 1_555 A A 10 1_555 -0.404 -1.866 3.145 -2.019 6.719 29.122 -4.867 0.405 2.678 13.122 3.943 29.937 14 AA_C33U34:A10G11_AA A 33 ? A 11 ? A 34 ? A 10 ? 1 A U 34 1_555 A A 10 1_555 A U 35 1_555 A A 9 1_555 0.152 -1.619 3.047 -0.075 15.235 20.558 -7.024 -0.360 1.504 36.851 0.182 25.539 15 AA_U34U35:A9A10_AA A 34 ? A 10 ? A 35 ? A 9 ? 1 A U 35 1_555 A A 9 1_555 A G 36 1_555 A G 31 1_555 2.803 -4.231 2.207 23.898 9.215 114.260 -2.562 -1.474 2.340 5.448 -14.130 116.092 16 AA_U35G36:G31A9_AA A 35 ? A 9 ? A 36 ? A 31 ? 1 A C 40 1_555 A G 47 1_555 A C 41 1_555 A G 46 1_555 -0.548 -2.413 3.295 -0.097 7.159 29.908 -5.849 1.016 2.661 13.627 0.185 30.734 17 AA_C40C41:G46G47_AA A 40 ? A 47 ? A 41 ? A 46 ? 1 A C 41 1_555 A G 46 1_555 A G 42 1_555 A A 45 1_555 -4.384 -1.561 2.859 0.219 10.594 52.611 -2.282 4.874 2.507 11.817 -0.244 53.593 18 AA_C41G42:A45G46_AA A 41 ? A 46 ? A 42 ? A 45 ? # _atom_sites.entry_id 3E5F _atom_sites.fract_transf_matrix[1][1] 0.010333 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.010333 _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] 0.011525 _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 N O P SE SR # loop_