data_3BNP # _entry.id 3BNP # _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 3BNP pdb_00003bnp 10.2210/pdb3bnp/pdb NDB AR0088 ? ? RCSB RCSB045741 ? ? WWPDB D_1000045741 ? ? # 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' # 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 # 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' # _pdbx_database_status.entry_id 3BNP _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 3BNL . unspecified PDB 3BNN . unspecified PDB 3BNO . 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 human mitochondrial ribosome, A chain' 7023.250 1 ? A1555G ? ? 2 polymer syn 'A site of human mitochondrial ribosome, B chain' 6718.068 1 ? A1555G ? ? 3 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 4 water nat water 18.015 13 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no CGCGUCACCCCGGGCAAGUCGC CGCGUCACCCCGGGCAAGUCGC A ? 2 polyribonucleotide no no GCGUCACCCCGGGCAAGUCGC GCGUCACCCCGGGCAAGUCGC B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'POTASSIUM ION' K 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C 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 C n 1 10 C n 1 11 C n 1 12 G n 1 13 G n 1 14 G n 1 15 C 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 2 1 G n 2 2 C n 2 3 G n 2 4 U n 2 5 C n 2 6 A n 2 7 C n 2 8 C n 2 9 C n 2 10 C n 2 11 G n 2 12 G n 2 13 G n 2 14 C n 2 15 A n 2 16 A n 2 17 G n 2 18 U n 2 19 C n 2 20 G n 2 21 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 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 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 C 1 1 1 C C 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 C 9 9 9 C C 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 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C 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 2 1 G 1 1 1 G G B . n B 2 2 C 2 2 2 C C B . n B 2 3 G 3 3 3 G G B . n B 2 4 U 4 4 4 U U B . n B 2 5 C 5 5 5 C C B . n B 2 6 A 6 6 6 A A B . n B 2 7 C 7 7 7 C C B . n B 2 8 C 8 8 8 C C B . n B 2 9 C 9 9 9 C C B . n B 2 10 C 10 10 10 C C B . n B 2 11 G 11 11 11 G G B . n B 2 12 G 12 12 12 G G B . n B 2 13 G 13 13 13 G G B . n B 2 14 C 14 14 14 C C B . n B 2 15 A 15 15 15 A A B . n B 2 16 A 16 16 16 A A B . n B 2 17 G 17 17 17 G G B . n B 2 18 U 18 18 18 U U B . n B 2 19 C 19 19 19 C C B . n B 2 20 G 20 20 20 G G B . n B 2 21 C 21 21 21 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 3 K 1 22 1 K K B . D 4 HOH 1 23 1 HOH HOH A . D 4 HOH 2 24 2 HOH HOH A . D 4 HOH 3 25 3 HOH HOH A . D 4 HOH 4 26 4 HOH HOH A . D 4 HOH 5 27 5 HOH HOH A . D 4 HOH 6 28 6 HOH HOH A . E 4 HOH 1 23 1 HOH HOH B . E 4 HOH 2 24 2 HOH HOH B . E 4 HOH 3 25 3 HOH HOH B . E 4 HOH 4 26 4 HOH HOH B . E 4 HOH 5 27 5 HOH HOH B . E 4 HOH 6 28 6 HOH HOH B . E 4 HOH 7 29 7 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 d*TREK 8.0SSI 'Feb 4 2003' package 'Pflugrath, J.W.' jwp@RigakuMSC.com 'data scaling' http://www.msc.com/protein/dtrek.html ? ? 1 AMoRE . ? program 'Jorge Navaza' ccp4@dl.ac.uk phasing http://www.ccp4.ac.uk/main.html Fortran_77 ? 2 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 3 PDB_EXTRACT 3.004 'September 10, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 4 # _cell.length_a 66.350 _cell.length_b 66.350 _cell.length_c 57.350 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3BNP _cell.Z_PDB 6 _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 'P 31 2 1' _symmetry.entry_id 3BNP _symmetry.Int_Tables_number 152 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3BNP _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.65 _exptl_crystal.density_percent_sol 53.62 _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, glycerol, paromomycin, 2-methyl-2,4-pentanediol, 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 2 MPD ? ? ? 1 5 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 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2004-03-17 _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 0.9801 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X10SA' _diffrn_source.pdbx_wavelength_list 0.9801 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X10SA # _reflns.entry_id 3BNP _reflns.d_resolution_high 2.700 _reflns.d_resolution_low 40.590 _reflns.number_obs 4215 _reflns.pdbx_scaling_rejects 317 _reflns.pdbx_Rmerge_I_obs 0.065 _reflns.pdbx_netI_over_sigmaI 22.000 _reflns.pdbx_chi_squared 0.990 _reflns.pdbx_redundancy 9.940 _reflns.percent_possible_obs 99.500 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _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 2.70 2.80 ? 4343 ? 0.362 3.9 ? 0.510 10.24 ? 424 100.00 ? 1 2.80 2.91 ? 4148 ? 0.228 5.9 ? 0.540 10.29 ? 403 100.00 ? 2 2.91 3.04 ? 4349 ? 0.145 8.7 ? 0.610 10.23 ? 425 100.00 ? 3 3.04 3.20 ? 4261 ? 0.096 13.6 ? 0.780 10.21 ? 415 100.00 ? 4 3.20 3.40 ? 4175 ? 0.080 18.0 ? 0.930 10.07 ? 412 100.00 ? 5 3.40 3.66 ? 4275 ? 0.087 20.0 ? 1.030 10.12 ? 416 100.00 ? 6 3.66 4.03 ? 4292 ? 0.077 25.9 ? 1.220 9.92 ? 425 100.00 ? 7 4.03 4.62 ? 4312 ? 0.068 34.1 ? 1.450 9.92 ? 431 100.00 ? 8 4.62 5.81 ? 4224 ? 0.049 44.7 ? 1.400 9.65 ? 433 100.00 ? 9 5.81 40.59 ? 3856 ? 0.046 48.1 ? 1.520 8.85 ? 431 94.10 ? 10 # _refine.entry_id 3BNP _refine.ls_d_res_high 2.700 _refine.ls_d_res_low 40.590 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.300 _refine.ls_number_reflns_obs 4204 _refine.ls_R_factor_R_work 0.231 _refine.ls_R_factor_R_free 0.270 _refine.ls_percent_reflns_R_free 10.200 _refine.ls_number_reflns_R_free 433 _refine.B_iso_mean 77.503 _refine.solvent_model_param_bsol 68.858 _refine.aniso_B[1][1] -8.620 _refine.aniso_B[2][2] -8.620 _refine.aniso_B[3][3] 17.241 _refine.aniso_B[1][2] -13.852 _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 0.775 _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.pdbx_overall_phase_error ? _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_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 908 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 13 _refine_hist.number_atoms_total 922 _refine_hist.d_res_high 2.700 _refine_hist.d_res_low 40.590 # 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 ? 0.005 1.500 ? 'X-RAY DIFFRACTION' ? c_angle_deg ? 1.0 2.000 ? '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 rna_free.param ? 'X-RAY DIFFRACTION' 2 CNS_TOPPAR:ion.param ? 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:water_rep.param ? 'X-RAY DIFFRACTION' # _struct.entry_id 3BNP _struct.title 'Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site (A1555G Mutant)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3BNP _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 2 ? C N N 3 ? D N N 4 ? E N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 3BNP 3BNP 1 ? ? ? 2 PDB 3BNP 3BNP 2 ? ? ? # 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 3BNP A 1 ? 22 ? 3BNP 1 ? 22 ? 1 22 2 2 3BNP B 1 ? 21 ? 3BNP 1 ? 21 ? 1 21 # _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 # _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 metalc1 metalc ? ? B A 16 OP2 ? ? ? 1_555 C K . K ? ? B A 16 B K 22 1_555 ? ? ? ? ? ? ? 2.439 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 2 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 2 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 2 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 20 N1 ? ? A C 3 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 20 O6 ? ? A C 3 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 20 N2 ? ? A C 3 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 19 N3 ? ? A G 4 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 19 O2 ? ? A G 4 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 19 N4 ? ? A G 4 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 N3 ? ? ? 1_555 B U 18 O4 ? ? A U 5 B U 18 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog11 hydrog ? ? A U 5 O2 ? ? ? 1_555 B U 18 N3 ? ? A U 5 B U 18 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog12 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 17 N1 ? ? A C 6 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 17 O6 ? ? A C 6 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 17 N2 ? ? A C 6 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 9 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 9 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 9 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 10 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 10 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 10 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 11 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 11 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 11 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 12 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 12 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 12 B C 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 13 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 13 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 13 B C 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 14 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 14 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 14 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 O2 ? ? ? 1_555 B C 7 N4 ? ? A C 15 B C 7 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog34 hydrog ? ? A G 18 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 18 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 18 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 18 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 18 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 18 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A U 19 N3 ? ? ? 1_555 B U 4 O2 ? ? A U 19 B U 4 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog38 hydrog ? ? A U 19 O4 ? ? ? 1_555 B U 4 N3 ? ? A U 19 B U 4 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog39 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 20 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 20 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 20 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 21 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 21 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 21 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 21 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 21 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 21 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 22 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 22 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 22 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 22 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 22 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 22 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 27 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _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 K K K N N 114 U OP3 O N N 115 U P P N N 116 U OP1 O N N 117 U OP2 O N N 118 U "O5'" O N N 119 U "C5'" C N N 120 U "C4'" C N R 121 U "O4'" O N N 122 U "C3'" C N S 123 U "O3'" O N N 124 U "C2'" C N R 125 U "O2'" O N N 126 U "C1'" C N R 127 U N1 N N N 128 U C2 C N N 129 U O2 O N N 130 U N3 N N N 131 U C4 C N N 132 U O4 O N N 133 U C5 C N N 134 U C6 C N N 135 U HOP3 H N N 136 U HOP2 H N N 137 U "H5'" H N N 138 U "H5''" H N N 139 U "H4'" H N N 140 U "H3'" H N N 141 U "HO3'" H N N 142 U "H2'" H N N 143 U "HO2'" H N N 144 U "H1'" H N N 145 U H3 H N N 146 U H5 H N N 147 U H6 H N N 148 # 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 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3BNP 'a-form double helix' 3BNP 'mismatched base pair' 3BNP 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 B C 21 1_555 -0.328 -0.175 0.249 -9.474 -2.825 1.080 1 A_G2:C21_B A 2 ? B 21 ? 19 1 1 A C 3 1_555 B G 20 1_555 0.404 -0.045 0.256 -1.390 -5.465 8.424 2 A_C3:G20_B A 3 ? B 20 ? 19 1 1 A G 4 1_555 B C 19 1_555 -0.089 -0.097 0.057 -0.849 -11.875 5.749 3 A_G4:C19_B A 4 ? B 19 ? 19 1 1 A U 5 1_555 B U 18 1_555 1.667 -1.875 0.212 0.170 -22.401 2.343 4 A_U5:U18_B A 5 ? B 18 ? 16 1 1 A C 6 1_555 B G 17 1_555 -0.292 0.046 0.120 0.795 -10.982 1.044 5 A_C6:G17_B A 6 ? B 17 ? 19 1 1 A C 9 1_555 B G 13 1_555 -0.139 0.120 0.542 5.463 0.417 6.383 6 A_C9:G13_B A 9 ? B 13 ? 19 1 1 A C 10 1_555 B G 12 1_555 -0.346 -0.158 -0.566 15.969 -18.043 5.568 7 A_C10:G12_B A 10 ? B 12 ? 19 1 1 A C 11 1_555 B G 11 1_555 0.016 -0.188 -0.118 5.411 -7.854 3.235 8 A_C11:G11_B A 11 ? B 11 ? 19 1 1 A G 12 1_555 B C 10 1_555 -0.037 -0.308 0.446 1.257 -5.043 -1.668 9 A_G12:C10_B A 12 ? B 10 ? 19 1 1 A G 13 1_555 B C 9 1_555 0.039 -0.048 -0.230 -8.117 -6.003 3.103 10 A_G13:C9_B A 13 ? B 9 ? 19 1 1 A G 14 1_555 B C 8 1_555 -0.043 -0.241 -0.245 -14.844 -12.582 1.770 11 A_G14:C8_B A 14 ? B 8 ? 19 1 1 A C 15 1_555 B C 7 1_555 6.919 -2.920 1.322 -12.189 1.321 -10.866 12 A_C15:C7_B A 15 ? B 7 ? ? ? 1 A G 18 1_555 B C 5 1_555 0.539 0.031 0.282 0.773 -1.738 2.154 13 A_G18:C5_B A 18 ? B 5 ? 19 1 1 A U 19 1_555 B U 4 1_555 -1.744 -1.639 0.389 3.872 -13.201 6.777 14 A_U19:U4_B A 19 ? B 4 ? 16 1 1 A C 20 1_555 B G 3 1_555 -0.035 -0.063 -0.381 9.815 -16.090 7.060 15 A_C20:G3_B A 20 ? B 3 ? 19 1 1 A G 21 1_555 B C 2 1_555 -0.109 -0.300 -0.122 -5.546 -9.674 0.470 16 A_G21:C2_B A 21 ? B 2 ? 19 1 1 A C 22 1_555 B G 1 1_555 0.148 -0.269 0.100 -2.409 2.246 -3.157 17 A_C22:G1_B A 22 ? B 1 ? 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 21 1_555 A C 3 1_555 B G 20 1_555 0.253 -1.936 3.125 1.707 0.291 33.494 -3.400 -0.171 3.117 0.504 -2.959 33.538 1 AA_G2C3:G20C21_BB A 2 ? B 21 ? A 3 ? B 20 ? 1 A C 3 1_555 B G 20 1_555 A G 4 1_555 B C 19 1_555 0.053 -2.135 3.204 1.437 3.955 24.118 -6.175 0.289 2.821 9.375 -3.407 24.477 2 AA_C3G4:C19G20_BB A 3 ? B 20 ? A 4 ? B 19 ? 1 A G 4 1_555 B C 19 1_555 A U 5 1_555 B U 18 1_555 -0.217 -1.042 3.247 -1.101 4.330 42.378 -1.861 0.190 3.135 5.970 1.518 42.602 3 AA_G4U5:U18C19_BB A 4 ? B 19 ? A 5 ? B 18 ? 1 A U 5 1_555 B U 18 1_555 A C 6 1_555 B G 17 1_555 0.172 -1.300 3.122 4.606 6.679 30.491 -3.533 0.471 2.777 12.425 -8.569 31.528 4 AA_U5C6:G17U18_BB A 5 ? B 18 ? A 6 ? B 17 ? 1 A C 9 1_555 B G 13 1_555 A C 10 1_555 B G 12 1_555 -0.687 -2.039 2.897 4.228 1.055 32.429 -3.777 1.850 2.722 1.878 -7.528 32.713 5 AA_C9C10:G12G13_BB A 9 ? B 13 ? A 10 ? B 12 ? 1 A C 10 1_555 B G 12 1_555 A C 11 1_555 B G 11 1_555 -0.463 -1.719 3.561 -4.802 8.887 32.946 -4.335 0.010 3.044 15.230 8.230 34.419 6 AA_C10C11:G11G12_BB A 10 ? B 12 ? A 11 ? B 11 ? 1 A C 11 1_555 B G 11 1_555 A G 12 1_555 B C 10 1_555 -0.164 -2.163 3.101 -5.085 5.017 31.867 -4.636 -0.504 2.731 8.997 9.118 32.637 7 AA_C11G12:C10G11_BB A 11 ? B 11 ? A 12 ? B 10 ? 1 A G 12 1_555 B C 10 1_555 A G 13 1_555 B C 9 1_555 0.330 -2.034 3.502 7.880 4.265 30.376 -4.553 0.915 3.178 7.925 -14.642 31.640 8 AA_G12G13:C9C10_BB A 12 ? B 10 ? A 13 ? B 9 ? 1 A G 13 1_555 B C 9 1_555 A G 14 1_555 B C 8 1_555 0.455 -2.061 3.444 6.819 8.003 32.564 -4.766 0.298 2.905 13.829 -11.783 34.175 9 AA_G13G14:C8C9_BB A 13 ? B 9 ? A 14 ? B 8 ? 1 A G 14 1_555 B C 8 1_555 A C 15 1_555 B C 7 1_555 -0.952 -1.211 3.163 -3.574 10.314 55.363 -1.833 0.817 2.964 10.982 3.805 56.345 10 AA_G14C15:C7C8_BB A 14 ? B 8 ? A 15 ? B 7 ? 1 A G 18 1_555 B C 5 1_555 A U 19 1_555 B U 4 1_555 0.058 -1.594 2.988 -6.347 8.516 29.256 -4.356 -1.138 2.377 16.203 12.075 31.085 11 AA_G18U19:U4C5_BB A 18 ? B 5 ? A 19 ? B 4 ? 1 A U 19 1_555 B U 4 1_555 A C 20 1_555 B G 3 1_555 -0.188 -1.035 3.088 3.395 5.999 39.266 -2.157 0.637 2.880 8.844 -5.005 39.843 12 AA_U19C20:G3U4_BB A 19 ? B 4 ? A 20 ? B 3 ? 1 A C 20 1_555 B G 3 1_555 A G 21 1_555 B C 2 1_555 -0.535 -1.705 3.597 -2.883 14.528 29.456 -5.476 0.456 2.539 26.561 5.272 32.897 13 AA_C20G21:C2G3_BB A 20 ? B 3 ? A 21 ? B 2 ? 1 A G 21 1_555 B C 2 1_555 A C 22 1_555 B G 1 1_555 0.174 -1.153 3.274 0.593 8.257 32.561 -3.296 -0.209 2.906 14.437 -1.037 33.569 14 AA_G21C22:G1C2_BB A 21 ? B 2 ? A 22 ? B 1 ? # _atom_sites.entry_id 3BNP _atom_sites.fract_transf_matrix[1][1] 0.015072 _atom_sites.fract_transf_matrix[1][2] 0.008702 _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] 0.017403 _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] 0.017437 _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 K N O P # loop_