data_3BNL # _entry.id 3BNL # _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 3BNL pdb_00003bnl 10.2210/pdb3bnl/pdb NDB AR0085 ? ? RCSB RCSB045737 ? ? WWPDB D_1000045737 ? ? # 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 2008-06-24 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_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_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3BNL _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 2007-12-14 _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.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 3BNN . unspecified PDB 3BNO . unspecified PDB 3BNP . unspecified PDB 3BNQ . unspecified PDB 3BNR . unspecified PDB 3BNS . unspecified PDB 3BNT . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Westhof, E.' 2 # _citation.id primary _citation.title 'The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 36 _citation.page_first 2654 _citation.page_last 2666 _citation.year 2008 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18346970 _citation.pdbx_database_id_DOI 10.1093/nar/gkn112 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Westhof, E.' 2 ? # 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 'A site of bacterial ribosome' 7049.243 2 ? ? ? ? 2 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 8 ? ? ? ? 3 water nat water 18.015 38 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UGCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can UGCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT HEXAMMINE(III)' NCO 3 water HOH # 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 G n 1 3 C n 1 4 G n 1 5 U n 1 6 C n 1 7 A n 1 8 C n 1 9 A n 1 10 C n 1 11 C n 1 12 G n 1 13 G n 1 14 U n 1 15 G n 1 16 A n 1 17 A n 1 18 G n 1 19 U n 1 20 C n 1 21 G n 1 22 C n # 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 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 U 1 1 1 U U A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 U 5 5 5 U U A . n A 1 6 C 6 6 6 C C A . n A 1 7 A 7 7 7 A A A . n A 1 8 C 8 8 8 C C A . n A 1 9 A 9 9 9 A A A . n A 1 10 C 10 10 10 C C A . n A 1 11 C 11 11 11 C C A . n A 1 12 G 12 12 12 G G A . n A 1 13 G 13 13 13 G G 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 A 16 16 16 A A A . n A 1 17 A 17 17 17 A A A . n A 1 18 G 18 18 18 G G A . n A 1 19 U 19 19 19 U U A . n A 1 20 C 20 20 20 C C A . n A 1 21 G 21 21 21 G G A . n A 1 22 C 22 22 22 C C A . n B 1 1 U 1 1 1 U U B . n B 1 2 G 2 2 2 G G B . n B 1 3 C 3 3 3 C C B . n B 1 4 G 4 4 4 G G B . n B 1 5 U 5 5 5 U U B . n B 1 6 C 6 6 6 C C B . n B 1 7 A 7 7 7 A A B . n B 1 8 C 8 8 8 C C B . n B 1 9 A 9 9 9 A A B . n B 1 10 C 10 10 10 C C B . n B 1 11 C 11 11 11 C C B . n B 1 12 G 12 12 12 G G B . n B 1 13 G 13 13 13 G G B . n B 1 14 U 14 14 14 U U B . n B 1 15 G 15 15 15 G G B . n B 1 16 A 16 16 16 A A B . n B 1 17 A 17 17 17 A A B . n B 1 18 G 18 18 18 G G B . n B 1 19 U 19 19 19 U U B . n B 1 20 C 20 20 20 C C B . n B 1 21 G 21 21 21 G G B . n B 1 22 C 22 22 22 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 NCO 1 23 1 NCO NCO A . D 2 NCO 1 24 1 NCO NCO A . E 2 NCO 1 25 1 NCO NCO A . F 2 NCO 1 23 1 NCO NCO B . G 2 NCO 1 24 1 NCO NCO B . H 2 NCO 1 25 1 NCO NCO B . I 2 NCO 1 26 1 NCO NCO B . J 2 NCO 1 27 1 NCO NCO B . K 3 HOH 1 26 1 HOH HOH A . K 3 HOH 2 27 2 HOH HOH A . K 3 HOH 3 28 3 HOH HOH A . K 3 HOH 4 29 4 HOH HOH A . K 3 HOH 5 30 5 HOH HOH A . K 3 HOH 6 31 6 HOH HOH A . K 3 HOH 7 32 7 HOH HOH A . K 3 HOH 8 33 8 HOH HOH A . K 3 HOH 9 34 9 HOH HOH A . K 3 HOH 10 35 10 HOH HOH A . K 3 HOH 11 36 11 HOH HOH A . K 3 HOH 12 37 12 HOH HOH A . K 3 HOH 13 38 13 HOH HOH A . K 3 HOH 14 39 14 HOH HOH A . K 3 HOH 15 40 15 HOH HOH A . K 3 HOH 16 41 16 HOH HOH A . K 3 HOH 17 42 17 HOH HOH A . K 3 HOH 18 43 18 HOH HOH A . K 3 HOH 19 44 19 HOH HOH A . K 3 HOH 20 45 20 HOH HOH A . K 3 HOH 21 46 21 HOH HOH A . L 3 HOH 1 28 1 HOH HOH B . L 3 HOH 2 29 2 HOH HOH B . L 3 HOH 3 30 3 HOH HOH B . L 3 HOH 4 31 4 HOH HOH B . L 3 HOH 5 32 5 HOH HOH B . L 3 HOH 6 33 6 HOH HOH B . L 3 HOH 7 34 7 HOH HOH B . L 3 HOH 8 35 8 HOH HOH B . L 3 HOH 9 36 9 HOH HOH B . L 3 HOH 10 37 10 HOH HOH B . L 3 HOH 11 38 11 HOH HOH B . L 3 HOH 12 39 12 HOH HOH B . L 3 HOH 13 40 13 HOH HOH B . L 3 HOH 14 41 14 HOH HOH B . L 3 HOH 15 42 15 HOH HOH B . L 3 HOH 16 43 16 HOH HOH B . L 3 HOH 17 44 17 HOH HOH B . # 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 MOSFLM . ? package 'A.G.W. Leslie' andrew@mrc-lmb.cam.ac.uk 'data reduction' http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ ? ? 1 SCALA . ? other 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/INDEX.html Fortran_77 ? 2 AMoRE . ? program 'Jorge Navaza' ccp4@dl.ac.uk phasing http://www.ccp4.ac.uk/main.html Fortran_77 ? 3 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 4 PDB_EXTRACT 3.004 'September 10, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 5 # _cell.length_a 73.599 _cell.length_b 73.599 _cell.length_c 63.496 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3BNL _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.space_group_name_H-M 'I 4' _symmetry.entry_id 3BNL _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 79 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3BNL _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.05 _exptl_crystal.density_percent_sol 59.67 _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.pH 7.0 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details ;Sodium cacodylate, KCl, 2-methyl-2,4-pentanediol, spermine tetrachloride, hexammine cobalt chloride, 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 MPD ? ? ? 1 2 1 KCl ? ? ? 1 3 1 'Sodium cacodylate' ? ? ? 1 4 1 '[Co(NH3)6]Cl3' ? ? ? 1 5 2 MPD ? ? ? 1 6 2 KCl ? ? ? # _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 2007-02-25 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.91636 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM30A' _diffrn_source.pdbx_wavelength_list 0.91636 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM30A # _reflns.entry_id 3BNL _reflns.d_resolution_high 2.602 _reflns.d_resolution_low 36.800 _reflns.number_obs 5295 _reflns.pdbx_Rmerge_I_obs 0.051 _reflns.pdbx_netI_over_sigmaI 9.400 _reflns.pdbx_Rsym_value 0.051 _reflns.pdbx_redundancy 7.100 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 2.602 2.74 ? 5724 ? 0.286 2.6 0.286 ? 7.30 ? 780 100.00 ? 1 2.74 2.91 ? 5283 ? 0.144 5.1 0.144 ? 7.30 ? 722 100.00 ? 2 2.91 3.11 ? 4927 ? 0.073 9.4 0.073 ? 7.30 ? 675 100.00 ? 3 3.11 3.36 ? 4711 ? 0.049 12.5 0.049 ? 7.30 ? 649 100.00 ? 4 3.36 3.68 ? 4149 ? 0.043 14.5 0.043 ? 7.20 ? 573 100.00 ? 5 3.68 4.11 ? 3787 ? 0.044 13.5 0.044 ? 7.10 ? 531 100.00 ? 6 4.11 4.75 ? 3304 ? 0.054 11.1 0.054 ? 7.00 ? 471 100.00 ? 7 4.75 5.81 ? 2684 ? 0.044 13.3 0.044 ? 6.70 ? 401 100.00 ? 8 5.81 8.22 ? 2062 ? 0.033 13.2 0.033 ? 6.60 ? 313 100.00 ? 9 8.22 36.80 ? 1116 ? 0.048 9.8 0.048 ? 6.20 ? 180 98.40 ? 10 # _refine.entry_id 3BNL _refine.ls_d_res_high 2.602 _refine.ls_d_res_low 36.000 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.700 _refine.ls_number_reflns_obs 5278 _refine.ls_R_factor_R_work 0.220 _refine.ls_R_factor_R_free 0.251 _refine.ls_percent_reflns_R_free 10.500 _refine.ls_number_reflns_R_free 556 _refine.B_iso_mean 44.093 _refine.solvent_model_param_bsol 181.362 _refine.aniso_B[1][1] -1.711 _refine.aniso_B[2][2] -1.711 _refine.aniso_B[3][3] 3.423 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.overall_FOM_work_R_set 0.811 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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.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_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 940 _refine_hist.pdbx_number_atoms_ligand 56 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 1034 _refine_hist.d_res_high 2.602 _refine_hist.d_res_low 36.000 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d ? 0.004 ? ? 'X-RAY DIFFRACTION' ? c_angle_deg ? 0.9 ? ? '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 CNS_TOPPAR:dna-rna_rep.param CNS_TOPPAR:dna-rna.top 'X-RAY DIFFRACTION' 2 nco_xplor.param nco_xplor.top 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:ion.param CNS_TOPPAR:ion.top 'X-RAY DIFFRACTION' 4 CNS_TOPPAR:water_rep.param CNS_TOPPAR:water.top 'X-RAY DIFFRACTION' # _struct.entry_id 3BNL _struct.title 'Crystal structure of the bacterial ribosomal decoding A site in the presence of [Co(NH3)6]Cl3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3BNL _struct_keywords.text 'ribosome, decoding site, 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 1 ? 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 3 ? L N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3BNL _struct_ref.pdbx_db_accession 3BNL _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 3BNL A 1 ? 22 ? 3BNL 1 ? 22 ? 1 22 2 1 3BNL B 1 ? 22 ? 3BNL 1 ? 22 ? 1 22 # _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # _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 hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 22 N3 ? ? A G 2 B C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 22 O2 ? ? A G 2 B C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 22 N4 ? ? A G 2 B C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 21 N1 ? ? A C 3 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 21 O6 ? ? A C 3 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 21 N2 ? ? A C 3 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 N3 ? ? ? 1_555 B U 19 O4 ? ? A U 5 B U 19 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog11 hydrog ? ? A U 5 O2 ? ? ? 1_555 B U 19 N3 ? ? A U 5 B U 19 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog12 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 18 N1 ? ? A C 6 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 18 O6 ? ? A C 6 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 18 N2 ? ? A C 6 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 7 N1 ? ? ? 1_555 B A 17 N6 ? ? A A 7 B A 17 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog16 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 8 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 8 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 8 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 14 N3 ? ? A A 9 B U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 14 O4 ? ? A A 9 B U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 10 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 10 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 10 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 11 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 11 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 11 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 12 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 12 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 12 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 13 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 13 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 13 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 14 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 14 B A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 14 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 14 B A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 15 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 15 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 15 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A A 17 N6 ? ? ? 1_555 B A 7 N1 ? ? A A 17 B A 7 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog39 hydrog ? ? A G 18 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 18 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 18 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 18 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 18 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 18 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A U 19 N3 ? ? ? 1_555 B U 5 O2 ? ? A U 19 B U 5 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog43 hydrog ? ? A U 19 O4 ? ? ? 1_555 B U 5 N3 ? ? A U 19 B U 5 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog44 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 21 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 21 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 21 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 21 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 21 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 21 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 22 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 22 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 22 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 22 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 22 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 22 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 NCO 23 ? 1 'BINDING SITE FOR RESIDUE NCO A 23' AC2 Software A NCO 24 ? 1 'BINDING SITE FOR RESIDUE NCO A 24' AC5 Software B NCO 24 ? 2 'BINDING SITE FOR RESIDUE NCO B 24' AC6 Software B NCO 25 ? 1 'BINDING SITE FOR RESIDUE NCO B 25' AC7 Software B NCO 26 ? 1 'BINDING SITE FOR RESIDUE NCO B 26' # 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 HOH K . ? HOH A 29 . ? 1_555 ? 2 AC2 1 HOH K . ? HOH A 30 . ? 1_555 ? 3 AC5 2 HOH K . ? HOH A 43 . ? 1_555 ? 4 AC5 2 HOH L . ? HOH B 44 . ? 1_555 ? 5 AC6 1 HOH L . ? HOH B 43 . ? 1_555 ? 6 AC7 1 HOH L . ? HOH B 42 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_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 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 P A U 1 ? ? OP3 A U 1 ? ? 1.521 1.607 -0.086 0.012 N 2 1 P B U 1 ? ? OP3 B U 1 ? ? 1.524 1.607 -0.083 0.012 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id U _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 5 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.087 _pdbx_validate_planes.type 'SIDE CHAIN' # _phasing.method MR # 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 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 NCO CO CO N N 114 NCO N1 N N N 115 NCO N2 N N N 116 NCO N3 N N N 117 NCO N4 N N N 118 NCO N5 N N N 119 NCO N6 N N N 120 NCO HN11 H N N 121 NCO HN12 H N N 122 NCO HN13 H N N 123 NCO HN21 H N N 124 NCO HN22 H N N 125 NCO HN23 H N N 126 NCO HN31 H N N 127 NCO HN32 H N N 128 NCO HN33 H N N 129 NCO HN41 H N N 130 NCO HN42 H N N 131 NCO HN43 H N N 132 NCO HN51 H N N 133 NCO HN52 H N N 134 NCO HN53 H N N 135 NCO HN61 H N N 136 NCO HN62 H N N 137 NCO HN63 H N N 138 U OP3 O N N 139 U P P N N 140 U OP1 O N N 141 U OP2 O N N 142 U "O5'" O N N 143 U "C5'" C N N 144 U "C4'" C N R 145 U "O4'" O N N 146 U "C3'" C N S 147 U "O3'" O N N 148 U "C2'" C N R 149 U "O2'" O N N 150 U "C1'" C N R 151 U N1 N N N 152 U C2 C N N 153 U O2 O N N 154 U N3 N N N 155 U C4 C N N 156 U O4 O N N 157 U C5 C N N 158 U C6 C N N 159 U HOP3 H N N 160 U HOP2 H N N 161 U "H5'" H N N 162 U "H5''" H N N 163 U "H4'" H N N 164 U "H3'" H N N 165 U "HO3'" H N N 166 U "H2'" H N N 167 U "HO2'" H N N 168 U "H1'" H N N 169 U H3 H N N 170 U H5 H N N 171 U H6 H N N 172 # 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 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 NCO CO N1 sing N N 118 NCO CO N2 sing N N 119 NCO CO N3 sing N N 120 NCO CO N4 sing N N 121 NCO CO N5 sing N N 122 NCO CO N6 sing N N 123 NCO N1 HN11 sing N N 124 NCO N1 HN12 sing N N 125 NCO N1 HN13 sing N N 126 NCO N2 HN21 sing N N 127 NCO N2 HN22 sing N N 128 NCO N2 HN23 sing N N 129 NCO N3 HN31 sing N N 130 NCO N3 HN32 sing N N 131 NCO N3 HN33 sing N N 132 NCO N4 HN41 sing N N 133 NCO N4 HN42 sing N N 134 NCO N4 HN43 sing N N 135 NCO N5 HN51 sing N N 136 NCO N5 HN52 sing N N 137 NCO N5 HN53 sing N N 138 NCO N6 HN61 sing N N 139 NCO N6 HN62 sing N N 140 NCO N6 HN63 sing N N 141 U OP3 P sing N N 142 U OP3 HOP3 sing N N 143 U P OP1 doub N N 144 U P OP2 sing N N 145 U P "O5'" sing N N 146 U OP2 HOP2 sing N N 147 U "O5'" "C5'" sing N N 148 U "C5'" "C4'" sing N N 149 U "C5'" "H5'" sing N N 150 U "C5'" "H5''" sing N N 151 U "C4'" "O4'" sing N N 152 U "C4'" "C3'" sing N N 153 U "C4'" "H4'" sing N N 154 U "O4'" "C1'" sing N N 155 U "C3'" "O3'" sing N N 156 U "C3'" "C2'" sing N N 157 U "C3'" "H3'" sing N N 158 U "O3'" "HO3'" sing N N 159 U "C2'" "O2'" sing N N 160 U "C2'" "C1'" sing N N 161 U "C2'" "H2'" sing N N 162 U "O2'" "HO2'" sing N N 163 U "C1'" N1 sing N N 164 U "C1'" "H1'" sing N N 165 U N1 C2 sing N N 166 U N1 C6 sing N N 167 U C2 O2 doub N N 168 U C2 N3 sing N N 169 U N3 C4 sing N N 170 U N3 H3 sing N N 171 U C4 O4 doub N N 172 U C4 C5 sing N N 173 U C5 C6 doub N N 174 U C5 H5 sing N N 175 U C6 H6 sing N N 176 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3BNL 'double helix' 3BNL 'a-form double helix' 3BNL 'bulge loop' 3BNL 'mismatched base pair' # 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 G 2 1_555 B C 22 1_555 -0.069 -0.218 0.208 2.471 -1.379 -2.599 1 A_G2:C22_B A 2 ? B 22 ? 19 1 1 A C 3 1_555 B G 21 1_555 0.497 -0.052 -0.122 11.536 -9.114 2.315 2 A_C3:G21_B A 3 ? B 21 ? 19 1 1 A G 4 1_555 B C 20 1_555 0.595 -0.215 0.371 6.234 -12.621 4.937 3 A_G4:C20_B A 4 ? B 20 ? 19 1 1 A U 5 1_555 B U 19 1_555 2.471 -1.952 0.088 1.603 -14.481 3.855 4 A_U5:U19_B A 5 ? B 19 ? 16 1 1 A C 6 1_555 B G 18 1_555 -0.032 -0.320 0.286 -10.674 -19.492 2.758 5 A_C6:G18_B A 6 ? B 18 ? 19 1 1 A A 7 1_555 B A 17 1_555 2.577 1.373 0.275 -24.756 -0.275 -14.269 6 A_A7:A17_B A 7 ? B 17 ? ? 1 1 A C 8 1_555 B G 15 1_555 0.176 -0.389 -0.017 -9.638 -5.227 0.012 7 A_C8:G15_B A 8 ? B 15 ? 19 1 1 A A 9 1_555 B U 14 1_555 0.197 -0.106 0.375 1.737 -12.010 6.411 8 A_A9:U14_B A 9 ? B 14 ? 20 1 1 A C 10 1_555 B G 13 1_555 0.251 -0.062 0.133 7.457 -11.232 1.495 9 A_C10:G13_B A 10 ? B 13 ? 19 1 1 A C 11 1_555 B G 12 1_555 0.022 -0.429 -0.007 3.225 -10.090 -1.106 10 A_C11:G12_B A 11 ? B 12 ? 19 1 1 A G 12 1_555 B C 11 1_555 0.780 -0.459 -0.164 -5.650 -7.474 -1.416 11 A_G12:C11_B A 12 ? B 11 ? 19 1 1 A G 13 1_555 B C 10 1_555 -0.081 -0.103 -0.020 -8.951 -14.882 2.275 12 A_G13:C10_B A 13 ? B 10 ? 19 1 1 A U 14 1_555 B A 9 1_555 -0.154 -0.083 0.461 -2.050 -11.249 6.664 13 A_U14:A9_B A 14 ? B 9 ? 20 1 1 A G 15 1_555 B C 8 1_555 -0.214 -0.424 -0.123 6.998 -6.320 1.001 14 A_G15:C8_B A 15 ? B 8 ? 19 1 1 A A 17 1_555 B A 7 1_555 -2.608 1.331 0.233 27.866 -0.550 -17.566 15 A_A17:A7_B A 17 ? B 7 ? ? ? 1 A G 18 1_555 B C 6 1_555 -0.164 -0.319 0.321 15.690 -18.356 2.275 16 A_G18:C6_B A 18 ? B 6 ? 19 1 1 A U 19 1_555 B U 5 1_555 -2.840 -2.063 0.162 2.442 -15.731 3.775 17 A_U19:U5_B A 19 ? B 5 ? 16 1 1 A C 20 1_555 B G 4 1_555 -0.291 -0.260 0.511 -5.336 -14.214 4.889 18 A_C20:G4_B A 20 ? B 4 ? 19 1 1 A G 21 1_555 B C 3 1_555 -0.190 -0.248 -0.179 -12.266 -9.834 0.056 19 A_G21:C3_B A 21 ? B 3 ? 19 1 1 A C 22 1_555 B G 2 1_555 0.352 -0.376 0.173 -1.147 -4.170 -5.202 20 A_C22:G2_B A 22 ? B 2 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 2 1_555 B C 22 1_555 A C 3 1_555 B G 21 1_555 -0.050 -1.126 3.156 2.122 -0.453 34.889 -1.809 0.393 3.161 -0.754 -3.535 34.954 1 AA_G2C3:G21C22_BB A 2 ? B 22 ? A 3 ? B 21 ? 1 A C 3 1_555 B G 21 1_555 A G 4 1_555 B C 20 1_555 -0.037 -1.823 3.284 -4.354 9.170 31.292 -4.681 -0.626 2.640 16.466 7.819 32.858 2 AA_C3G4:C20G21_BB A 3 ? B 21 ? A 4 ? B 20 ? 1 A G 4 1_555 B C 20 1_555 A U 5 1_555 B U 19 1_555 -0.160 -1.120 3.282 2.060 4.901 44.989 -1.884 0.388 3.139 6.378 -2.681 45.286 3 AA_G4U5:U19C20_BB A 4 ? B 20 ? A 5 ? B 19 ? 1 A U 5 1_555 B U 19 1_555 A C 6 1_555 B G 18 1_555 0.254 -1.805 3.261 6.557 7.629 28.665 -4.888 0.752 2.693 14.844 -12.757 30.344 4 AA_U5C6:G18U19_BB A 5 ? B 19 ? A 6 ? B 18 ? 1 A C 6 1_555 B G 18 1_555 A A 7 1_555 B A 17 1_555 -0.664 -1.551 3.425 5.642 8.289 41.131 -2.992 1.492 2.960 11.592 -7.889 42.284 5 AA_C6A7:A17G18_BB A 6 ? B 18 ? A 7 ? B 17 ? 1 A A 7 1_555 B A 17 1_555 A C 8 1_555 B G 15 1_555 3.668 -0.276 3.707 -5.789 14.858 39.822 -1.938 -5.636 2.894 20.830 8.116 42.775 6 AA_A7C8:G15A17_BB A 7 ? B 17 ? A 8 ? B 15 ? 1 A C 8 1_555 B G 15 1_555 A A 9 1_555 B U 14 1_555 0.647 -1.406 2.657 -2.805 15.382 31.031 -4.039 -1.391 1.726 26.730 4.874 34.661 7 AA_C8A9:U14G15_BB A 8 ? B 15 ? A 9 ? B 14 ? 1 A A 9 1_555 B U 14 1_555 A C 10 1_555 B G 13 1_555 -0.586 -1.021 3.121 0.004 5.652 30.030 -2.978 1.114 2.885 10.788 -0.008 30.545 8 AA_A9C10:G13U14_BB A 9 ? B 14 ? A 10 ? B 13 ? 1 A C 10 1_555 B G 13 1_555 A C 11 1_555 B G 12 1_555 -0.385 -1.776 3.261 -0.585 6.929 31.978 -4.281 0.588 2.830 12.394 1.047 32.706 9 AA_C10C11:G12G13_BB A 10 ? B 13 ? A 11 ? B 12 ? 1 A C 11 1_555 B G 12 1_555 A G 12 1_555 B C 11 1_555 -0.153 -1.449 3.414 1.404 12.714 37.377 -3.614 0.389 2.786 19.165 -2.116 39.431 10 AA_C11G12:C11G12_BB A 11 ? B 12 ? A 12 ? B 11 ? 1 A G 12 1_555 B C 11 1_555 A G 13 1_555 B C 10 1_555 0.484 -1.726 3.245 0.887 8.881 29.558 -4.835 -0.751 2.640 16.927 -1.690 30.848 11 AA_G12G13:C10C11_BB A 12 ? B 11 ? A 13 ? B 10 ? 1 A G 13 1_555 B C 10 1_555 A U 14 1_555 B A 9 1_555 0.367 -1.011 3.043 -2.744 5.330 29.425 -2.937 -1.216 2.776 10.359 5.332 30.016 12 AA_G13U14:A9C10_BB A 13 ? B 10 ? A 14 ? B 9 ? 1 A U 14 1_555 B A 9 1_555 A G 15 1_555 B C 8 1_555 -0.588 -1.464 2.718 4.331 15.125 30.368 -4.226 1.498 1.720 26.736 -7.657 34.116 13 AA_U14G15:C8A9_BB A 14 ? B 9 ? A 15 ? B 8 ? 1 A G 15 1_555 B C 8 1_555 A A 17 1_555 B A 7 1_555 -3.890 -0.294 3.612 5.582 13.533 39.894 -1.810 5.958 2.827 19.073 -7.867 42.392 14 AA_G15A17:A7C8_BB A 15 ? B 8 ? A 17 ? B 7 ? 1 A A 17 1_555 B A 7 1_555 A G 18 1_555 B C 6 1_555 0.957 -1.686 3.408 -5.341 7.821 40.934 -3.149 -1.880 2.910 11.006 7.516 41.969 15 AA_A17G18:C6A7_BB A 17 ? B 7 ? A 18 ? B 6 ? 1 A G 18 1_555 B C 6 1_555 A U 19 1_555 B U 5 1_555 -0.198 -1.805 3.129 -6.863 8.838 28.136 -5.043 -0.850 2.443 17.336 13.463 30.238 16 AA_G18U19:U5C6_BB A 18 ? B 6 ? A 19 ? B 5 ? 1 A U 19 1_555 B U 5 1_555 A C 20 1_555 B G 4 1_555 0.284 -1.149 3.429 -1.317 3.420 46.860 -1.732 -0.468 3.333 4.293 1.653 46.995 17 AA_U19C20:G4U5_BB A 19 ? B 5 ? A 20 ? B 4 ? 1 A C 20 1_555 B G 4 1_555 A G 21 1_555 B C 3 1_555 -0.284 -1.799 3.354 6.298 9.986 32.105 -4.548 1.420 2.595 17.341 -10.937 34.153 18 AA_C20G21:C3G4_BB A 20 ? B 4 ? A 21 ? B 3 ? 1 A G 21 1_555 B C 3 1_555 A C 22 1_555 B G 2 1_555 0.144 -1.278 3.132 -2.219 0.406 34.563 -2.207 -0.567 3.103 0.682 3.729 34.634 19 AA_G21C22:G2C3_BB A 21 ? B 3 ? A 22 ? B 2 ? # _atom_sites.entry_id 3BNL _atom_sites.fract_transf_matrix[1][1] 0.013587 _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] 0.013587 _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] 0.015749 _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 # loop_