data_1QKG # _entry.id 1QKG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 1QKG pdb_00001qkg 10.2210/pdb1qkg/pdb PDBE EBI-2961 ? ? WWPDB D_1290002961 ? ? BMRB 4409 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1CFL unspecified 'DNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT' BMRB 4409 unspecified . # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1QKG _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 1999-07-20 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Lee, J.-H.' 1 'Bae, S.-H.' 2 'Choi, Y.-J.' 3 'Choi, B.-S.' 4 # _citation.id primary _citation.title ;The Dewar Photoproduct of Thymidylyl(3'-->5')-Thymidine (Dewar Product) Exhibits Mutagenic Behavior in Accordance with the "A Rule". ; _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 97 _citation.page_first 4591 _citation.page_last ? _citation.year 2000 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10758155 _citation.pdbx_database_id_DOI 10.1073/PNAS.080057097 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lee, J.-H.' 1 ? primary 'Bae, S.-H.' 2 ? primary 'Choi, B.-S.' 3 ? # _cell.entry_id 1QKG _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QKG _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # 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 ;DNA (5'-D(*CP*GP*CP*AP*(HYD)TP*+TP*AP*CP*GP*C)-3') ; 3009.014 1 ? ? ? 'BOND FORMED BETWEEN C6(T5) AND C4(T6) BOND FORMED BETWEEN N3(T6) AND C6(T6)' 2 polymer syn ;DNA (5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3') ; 3101.028 1 ? ? ? ? # 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 polydeoxyribonucleotide no yes '(DC)(DG)(DC)(DA)(64T)(TA3)(DA)(DC)(DG)(DC)' CGCATTACGC A ? 2 polydeoxyribonucleotide no no '(DG)(DC)(DG)(DT)(DG)(DA)(DT)(DG)(DC)(DG)' GCGTGATGCG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DA n 1 5 64T n 1 6 TA3 n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n 2 1 DG n 2 2 DC n 2 3 DG n 2 4 DT n 2 5 DG n 2 6 DA n 2 7 DT n 2 8 DG n 2 9 DC n 2 10 DG n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 1QKG 1 ? ? 1QKG ? 2 PDB 1QKG 2 ? ? 1QKG ? # 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 1QKG A 1 ? 10 ? 1QKG 1 ? 10 ? 1 10 2 2 1QKG B 1 ? 10 ? 1QKG 11 ? 20 ? 11 20 # 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 64T 'DNA linking' n "5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H17 N2 O9 P' 340.224 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 TA3 'DNA linking' n '(4S,5R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYL-1,3-DIAZABICYCLO[2.2.0]HEXAN-2-ONE' ? 'C10 H17 N2 O7 P' 308.225 # _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.type NOESY _pdbx_nmr_exptl.solution_id 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 274.0 _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.6 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '100% D2O, 10% WATER/90% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model DMX _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1QKG _pdbx_nmr_refine.method 'SIMULATED ANNEALING AND FULL RELAXATION MATRIX REFINEMENT' _pdbx_nmr_refine.details ;RESTRAINED MOLECULAR DYNAMICS WITH NMR-DERIVEN DISTANCE RESTRAINTS AND THEN FULL RELAXATION MATRIX REFINEMENT WITH NOE VOLUME ITENSITY RESTRAINTS ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1QKG _pdbx_nmr_details.text ;MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING SA METHOD WITH DISTANCE RESTRAINTS AND FULL RELAXATION MATRIX REFINEMENT WITH NOE INTENSITY RESTRAINTS OF 50, 80, 160 MS MIXING TIMES ; # _pdbx_nmr_ensemble.entry_id 1QKG _pdbx_nmr_ensemble.conformers_calculated_total_number 8 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'LEAST RESTRAINT VIOLATION' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR 3.1 BRUNGER 1 'structure solution' X-PLOR ? ? 2 # _exptl.entry_id 1QKG _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1QKG _struct.title 'DNA DECAMER DUPLEX CONTAINING T-T DEWAR PHOTOPRODUCT' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'MINIMIZED AVERAGE' # _struct_keywords.entry_id 1QKG _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DEOXYRIBONUCLEIC ACID, DNA PHOTOPRODUCT, DEWAR PRODUCT, (6-4) ADDUCT, MUTAGENESIS, TRANSLESION REPLICATION, DNA' # 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 ? # _struct_biol.id 1 # 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 DA 4 "O3'" ? ? ? 1_555 A 64T 5 P ? ? A DA 4 A 64T 5 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale2 covale both ? A 64T 5 "O3'" ? ? ? 1_555 A TA3 6 P ? ? A 64T 5 A TA3 6 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale3 covale none ? A 64T 5 C6 ? ? ? 1_555 A TA3 6 C4 ? ? A 64T 5 A TA3 6 1_555 ? ? ? ? ? ? ? 1.501 ? ? covale4 covale both ? A TA3 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A TA3 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.601 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 8 N1 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 8 O6 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 8 N2 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1QKG _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1QKG _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _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 H N O P # 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 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 64T 5 5 5 64T 64T A . n A 1 6 TA3 6 6 6 TA3 TA3 A . n A 1 7 DA 7 7 7 DA DA A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DC 10 10 10 DC DC A . n B 2 1 DG 1 11 11 DG DG B . n B 2 2 DC 2 12 12 DC DC B . n B 2 3 DG 3 13 13 DG DG B . n B 2 4 DT 4 14 14 DT DT B . n B 2 5 DG 5 15 15 DG DG B . n B 2 6 DA 6 16 16 DA DA B . n B 2 7 DT 7 17 17 DT DT B . n B 2 8 DG 8 18 18 DG DG B . n B 2 9 DC 9 19 19 DC DC B . n B 2 10 DG 10 20 20 DG DG B . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 64T 5 A 64T 5 ? DT "5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE" 2 A TA3 6 A TA3 6 ? DT ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details 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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1890 ? 1 MORE 2 ? 1 'SSA (A^2)' 3760 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2000-05-11 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2020-01-15 5 'Structure model' 1 4 2023-06-14 # _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' 'Version format compliance' 3 4 'Structure model' 'Derived calculations' 4 4 'Structure model' Other 5 5 'Structure model' 'Database references' 6 5 'Structure model' Other # 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 4 'Structure model' pdbx_database_status 2 4 'Structure model' struct_conn 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_database_status # 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 4 'Structure model' '_pdbx_database_status.status_code_cs' 2 4 'Structure model' '_pdbx_database_status.status_code_mr' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_pdbx_database_status.status_code_nmr_data' # _pdbx_entry_details.entry_id 1QKG _pdbx_entry_details.compound_details ;MISMATCHED BASE PAIRING OF 3'-T OF DEWAR PRODUCT WITH G RESIDUE ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 N9 A DA 4 ? ? C4 A DA 4 ? ? 1.413 1.374 0.039 0.006 N 2 1 N1 B DT 17 ? ? C2 B DT 17 ? ? 1.429 1.376 0.053 0.008 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.57 108.30 3.27 0.30 N 2 1 "C3'" A DG 2 ? ? "O3'" A DG 2 ? ? P A DC 3 ? ? 132.30 119.70 12.60 1.20 Y 3 1 N1 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 122.56 118.90 3.66 0.60 N 4 1 "C3'" A DC 3 ? ? "O3'" A DC 3 ? ? P A DA 4 ? ? 141.19 119.70 21.49 1.20 Y 5 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 110.15 108.30 1.85 0.30 N 6 1 "C3'" A DA 4 ? ? "O3'" A DA 4 ? ? P A 64T 5 ? ? 128.70 119.70 9.00 1.20 Y 7 1 "C3'" A 64T 5 ? ? "O3'" A 64T 5 ? ? P A TA3 6 ? ? 127.24 119.70 7.54 1.20 Y 8 1 "C3'" A TA3 6 ? ? "O3'" A TA3 6 ? ? P A DA 7 ? ? 128.96 119.70 9.26 1.20 Y 9 1 "C3'" A DA 7 ? ? "O3'" A DA 7 ? ? P A DC 8 ? ? 128.61 119.70 8.91 1.20 Y 10 1 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 122.91 118.90 4.01 0.60 N 11 1 "C3'" A DC 8 ? ? "O3'" A DC 8 ? ? P A DG 9 ? ? 127.93 119.70 8.23 1.20 Y 12 1 C2 A DG 9 ? ? N3 A DG 9 ? ? C4 A DG 9 ? ? 115.05 111.90 3.15 0.50 N 13 1 "C3'" A DG 9 ? ? "O3'" A DG 9 ? ? P A DC 10 ? ? 136.21 119.70 16.51 1.20 Y 14 1 "C1'" B DG 11 ? ? "O4'" B DG 11 ? ? "C4'" B DG 11 ? ? 102.82 110.10 -7.28 1.00 N 15 1 "O4'" B DG 11 ? ? "C1'" B DG 11 ? ? N9 B DG 11 ? ? 111.30 108.30 3.00 0.30 N 16 1 C2 B DG 11 ? ? N3 B DG 11 ? ? C4 B DG 11 ? ? 114.93 111.90 3.03 0.50 N 17 1 "C3'" B DG 11 ? ? "O3'" B DG 11 ? ? P B DC 12 ? ? 136.71 119.70 17.01 1.20 Y 18 1 "C3'" B DC 12 ? ? "O3'" B DC 12 ? ? P B DG 13 ? ? 128.26 119.70 8.56 1.20 Y 19 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? "C2'" B DG 13 ? ? 99.98 105.90 -5.92 0.80 N 20 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 112.83 108.30 4.53 0.30 N 21 1 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DT 14 ? ? 130.89 119.70 11.19 1.20 Y 22 1 P B DT 14 ? ? "O5'" B DT 14 ? ? "C5'" B DT 14 ? ? 130.90 120.90 10.00 1.60 N 23 1 N3 B DG 15 ? ? C2 B DG 15 ? ? N2 B DG 15 ? ? 127.28 119.90 7.38 0.70 N 24 1 "C3'" B DG 15 ? ? "O3'" B DG 15 ? ? P B DA 16 ? ? 127.08 119.70 7.38 1.20 Y 25 1 "C1'" B DA 16 ? ? "O4'" B DA 16 ? ? "C4'" B DA 16 ? ? 103.27 110.10 -6.83 1.00 N 26 1 "O4'" B DA 16 ? ? "C1'" B DA 16 ? ? N9 B DA 16 ? ? 113.75 108.30 5.45 0.30 N 27 1 "C3'" B DA 16 ? ? "O3'" B DA 16 ? ? P B DT 17 ? ? 135.40 119.70 15.70 1.20 Y 28 1 "C3'" B DT 17 ? ? "O3'" B DT 17 ? ? P B DG 18 ? ? 138.14 119.70 18.44 1.20 Y 29 1 C2 B DG 18 ? ? N3 B DG 18 ? ? C4 B DG 18 ? ? 115.27 111.90 3.37 0.50 N 30 1 "C3'" B DG 18 ? ? "O3'" B DG 18 ? ? P B DC 19 ? ? 137.33 119.70 17.63 1.20 Y 31 1 "C3'" B DC 19 ? ? "O3'" B DC 19 ? ? P B DG 20 ? ? 127.42 119.70 7.72 1.20 Y 32 1 "O4'" B DG 20 ? ? "C1'" B DG 20 ? ? N9 B DG 20 ? ? 110.27 108.30 1.97 0.30 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1QKG 'double helix' 1QKG 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 10 1_555 0.469 -0.209 -0.370 2.970 -14.615 -0.392 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DG 2 1_555 B DC 9 1_555 0.200 -0.142 -0.088 -1.344 -6.574 -4.510 2 A_DG2:DC19_B A 2 ? B 19 ? 19 1 1 A DC 3 1_555 B DG 8 1_555 0.063 -0.143 0.600 -11.914 5.273 -3.465 3 A_DC3:DG18_B A 3 ? B 18 ? 19 1 1 A DA 4 1_555 B DT 7 1_555 0.134 0.051 0.316 26.621 -16.615 -3.966 4 A_DA4:DT17_B A 4 ? B 17 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.191 -0.208 0.532 -9.082 -11.110 -1.155 5 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 -0.003 -0.081 0.040 3.655 -1.871 -7.470 6 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.059 -0.116 -0.425 4.266 -8.003 -3.162 7 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.335 -0.147 -0.074 -5.215 1.012 -3.487 8 A_DC10:DG11_B A 10 ? B 11 ? 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 DC 1 1_555 B DG 10 1_555 A DG 2 1_555 B DC 9 1_555 -0.288 -1.188 3.270 0.396 16.569 25.997 -5.162 0.613 2.141 32.916 -0.787 30.754 1 AA_DC1DG2:DC19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DG 2 1_555 B DC 9 1_555 A DC 3 1_555 B DG 8 1_555 -0.425 -0.941 3.410 -5.326 4.440 39.950 -1.873 -0.003 3.318 6.439 7.724 40.523 2 AA_DG2DC3:DG18DC19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DC 3 1_555 B DG 8 1_555 A DA 4 1_555 B DT 7 1_555 -0.152 -0.221 2.402 4.307 -2.587 26.238 0.016 1.152 2.357 -5.633 -9.378 26.706 3 AA_DC3DA4:DT17DG18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 -0.341 -0.235 3.066 1.303 -4.513 34.019 0.267 0.769 3.056 -7.668 -2.214 34.332 4 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.219 -1.159 3.139 2.657 13.916 25.623 -4.934 0.937 2.197 28.747 -5.488 29.221 5 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 -0.130 -1.185 3.494 -3.999 -1.632 41.262 -1.486 -0.275 3.534 -2.308 5.656 41.478 6 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? #