data_1DJD # _entry.id 1DJD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1DJD pdb_00001djd 10.2210/pdb1djd/pdb RCSB RCSB010129 ? ? WWPDB D_1000010129 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DJD _pdbx_database_status.recvd_initial_deposition_date 1999-12-02 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Li, Z.' 1 'Kim, H.Y.' 2 'Tamura, P.J.' 3 'Harris, C.M.' 4 'Harris, T.M.' 5 'Stone, M.P.' 6 # _citation.id primary _citation.title ;Role of a polycyclic aromatic hydrocarbon bay region ring in modulating DNA adduct structure: the non-bay region (8S,9R,10S, 11R)-N(6)-[11-(8,9,10,11-tetrahydro-8,9, 10-trihydroxybenz[a]anthracenyl)]-2' -deoxyadenosyl adduct in codon 61 of the human N-ras protooncogene ; _citation.journal_abbrev Biochemistry _citation.journal_volume 38 _citation.page_first 14820 _citation.page_last 14832 _citation.year 1999 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10555964 _citation.pdbx_database_id_DOI 10.1021/bi991607z # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Li, Z.' 1 ? primary 'Kim, H.Y.' 2 ? primary 'Tamura, P.J.' 3 ? primary 'Harris, C.M.' 4 ? primary 'Harris, T.M.' 5 ? primary 'Stone, M.P.' 6 ? # _cell.entry_id 1DJD _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 1DJD _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(*CT*GT*GT*AT*CT*AT*AT*GT*AT*AT*G)-3')" 3416.263 1 ? ? ? ? 2 polymer syn "DNA(5'-D(*CT*TT*TT*CT*TT*TT*GT*TT*CT*CT*G)-3')" 3291.145 1 ? ? ? ? 3 non-polymer syn '8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL' 280.318 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 no '(DC)(DG)(DG)(DA)(DC)(DA)(DA)(DG)(DA)(DA)(DG)' CGGACAAGAAG A ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DT)(DC)(DT)(DT)(DG)(DT)(DC)(DC)(DG)' CTTCTTGTCCG 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 DG n 1 4 DA n 1 5 DC n 1 6 DA n 1 7 DA n 1 8 DG n 1 9 DA n 1 10 DA n 1 11 DG n 2 1 DC n 2 2 DT n 2 3 DT n 2 4 DC n 2 5 DT n 2 6 DT n 2 7 DG n 2 8 DT n 2 9 DC n 2 10 DC n 2 11 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Sequence Observed In human N-ras codon 61' # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1DJD 1DJD ? ? ? 2 2 PDB 1DJD 1DJD ? ? ? # 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 1DJD A 1 ? 11 ? 1DJD 1 ? 11 ? 1 11 2 2 1DJD B 1 ? 11 ? 1DJD 12 ? 22 ? 12 22 # 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 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 TBT non-polymer . '8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL' ? 'C18 H16 O3' 280.318 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 2 2 '2D NOESY' 3 2 2 DQF-COSY 4 2 2 TOCSY # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 278 1 7.0 '0.1 M NaCl' atm K 2 293 1 7.0 '0.1 M NaCl' atm K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1.8 mM oligodeoxynucleotide; 10 mM phosphate buffer; 0.05 mM EDTA; 0.1 M NaCl' '90% H2O/10% D2O' 2 '1.8 mM oligodeoxynucleotide; 10 mM phosphate buffer; 0.05 mM EDTA; 0.1 M NaCl' '100% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Bruker DMX 500 2 ? Bruker DMX 750 # _pdbx_nmr_refine.entry_id 1DJD _pdbx_nmr_refine.method 'NOE-restrained molecular dynamics/simulated annealing' _pdbx_nmr_refine.details ;The structure is based on a total of 475 NOE derived distance constraints, 55 empirical sugar pucker restraints, 35 empirical backbone angle restraints, and 18 empirical planarity restraints. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1DJD _pdbx_nmr_details.text 'This structure was determined using 2D homonuclear techniques' # _pdbx_nmr_ensemble.entry_id 1DJD _pdbx_nmr_ensemble.conformers_calculated_total_number 1 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'back calculated data agree with experimental NOESY spectrum' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1DJD _pdbx_nmr_representative.conformer_id 12 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal XwinNMR 2.0 collection Bruker 1 X-PLOR 3.851 'structure solution' Brunger 2 Felix 97.0 processing 'Biosym Technologies' 3 CORMA 5.2 refinement 'Borgias, Thomas, Li, Kumar, Tonelli' 4 MARDIGRAS 3.0 'iterative matrix relaxation' 'Borgias, Thomas, Li, Kumar, Tonelli' 5 # _exptl.entry_id 1DJD _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1DJD _struct.title ;THE SOLUTION STRUCTURE OF A NON-BAY REGION 11R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DJD _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'BENZ[A]ANTHRACENE-DNA DUPLEX, 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 ? C N N 3 ? # _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 none ? A DA 6 N6 ? ? ? 1_555 C TBT . C4C ? ? A DA 6 A TBT 25 1_555 ? ? ? ? ? ? ? 1.343 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 1 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 1 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 1 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 2 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 2 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 2 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 3 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 3 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 3 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 4 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 4 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 5 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 5 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 5 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 6 B DT 17 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 7 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 7 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 8 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 8 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 8 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 8 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 8 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 9 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 9 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 10 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 10 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id TBT _struct_site.pdbx_auth_seq_id 25 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'BINDING SITE FOR RESIDUE TBT A 25' # 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 5 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 5 DA A 7 ? DA A 7 . ? 1_555 ? 3 AC1 5 DT B 5 ? DT B 16 . ? 1_555 ? 4 AC1 5 DT B 6 ? DT B 17 . ? 1_555 ? 5 AC1 5 DG B 7 ? DG B 18 . ? 1_555 ? # _database_PDB_matrix.entry_id 1DJD _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 1DJD _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 C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DA 6 6 6 DA ABA A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DA 9 9 9 DA A A . n A 1 10 DA 10 10 10 DA A A . n A 1 11 DG 11 11 11 DG G A . n B 2 1 DC 1 12 12 DC C B . n B 2 2 DT 2 13 13 DT T B . n B 2 3 DT 3 14 14 DT T B . n B 2 4 DC 4 15 15 DC C B . n B 2 5 DT 5 16 16 DT T B . n B 2 6 DT 6 17 17 DT T B . n B 2 7 DG 7 18 18 DG G B . n B 2 8 DT 8 19 19 DT T B . n B 2 9 DC 9 20 20 DC C B . n B 2 10 DC 10 21 21 DC C B . n B 2 11 DG 11 22 22 DG G B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id TBT _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 25 _pdbx_nonpoly_scheme.auth_seq_num 6 _pdbx_nonpoly_scheme.pdb_mon_id TBT _pdbx_nonpoly_scheme.auth_mon_id ABA _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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 1999-12-16 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 4 'Structure model' struct_conn 6 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 17 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 18 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 19 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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 ? ? 111.63 108.30 3.33 0.30 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.27 108.30 2.97 0.30 N 3 1 N7 A DG 2 ? ? C8 A DG 2 ? ? N9 A DG 2 ? ? 117.59 113.10 4.49 0.50 N 4 1 C8 A DG 2 ? ? N9 A DG 2 ? ? C4 A DG 2 ? ? 103.63 106.40 -2.77 0.40 N 5 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 110.77 108.30 2.47 0.30 N 6 1 N7 A DG 3 ? ? C8 A DG 3 ? ? N9 A DG 3 ? ? 117.69 113.10 4.59 0.50 N 7 1 C8 A DG 3 ? ? N9 A DG 3 ? ? C4 A DG 3 ? ? 103.76 106.40 -2.64 0.40 N 8 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.41 108.30 3.11 0.30 N 9 1 N7 A DA 4 ? ? C8 A DA 4 ? ? N9 A DA 4 ? ? 117.50 113.80 3.70 0.50 N 10 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.24 108.30 2.94 0.30 N 11 1 N7 A DA 6 ? ? C8 A DA 6 ? ? N9 A DA 6 ? ? 117.62 113.80 3.82 0.50 N 12 1 "O4'" A DA 7 ? ? "C1'" A DA 7 ? ? N9 A DA 7 ? ? 111.47 108.30 3.17 0.30 N 13 1 N7 A DA 7 ? ? C8 A DA 7 ? ? N9 A DA 7 ? ? 117.68 113.80 3.88 0.50 N 14 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.32 108.30 3.02 0.30 N 15 1 N7 A DG 8 ? ? C8 A DG 8 ? ? N9 A DG 8 ? ? 117.67 113.10 4.57 0.50 N 16 1 C8 A DG 8 ? ? N9 A DG 8 ? ? C4 A DG 8 ? ? 103.74 106.40 -2.66 0.40 N 17 1 N7 A DA 9 ? ? C8 A DA 9 ? ? N9 A DA 9 ? ? 117.46 113.80 3.66 0.50 N 18 1 "O4'" A DA 10 ? ? "C1'" A DA 10 ? ? N9 A DA 10 ? ? 110.78 108.30 2.48 0.30 N 19 1 N7 A DA 10 ? ? C8 A DA 10 ? ? N9 A DA 10 ? ? 117.61 113.80 3.81 0.50 N 20 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 111.07 108.30 2.77 0.30 N 21 1 N7 A DG 11 ? ? C8 A DG 11 ? ? N9 A DG 11 ? ? 117.94 113.10 4.84 0.50 N 22 1 C8 A DG 11 ? ? N9 A DG 11 ? ? C4 A DG 11 ? ? 103.73 106.40 -2.67 0.40 N 23 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 111.51 108.30 3.21 0.30 N 24 1 "O4'" B DT 13 ? ? "C1'" B DT 13 ? ? N1 B DT 13 ? ? 111.00 108.30 2.70 0.30 N 25 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 111.33 108.30 3.03 0.30 N 26 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 111.57 108.30 3.27 0.30 N 27 1 "O4'" B DT 16 ? ? "C1'" B DT 16 ? ? N1 B DT 16 ? ? 111.43 108.30 3.13 0.30 N 28 1 C6 B DT 16 ? ? C5 B DT 16 ? ? C7 B DT 16 ? ? 119.25 122.90 -3.65 0.60 N 29 1 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 111.04 108.30 2.74 0.30 N 30 1 "O4'" B DG 18 ? ? "C1'" B DG 18 ? ? N9 B DG 18 ? ? 110.59 108.30 2.29 0.30 N 31 1 N7 B DG 18 ? ? C8 B DG 18 ? ? N9 B DG 18 ? ? 117.62 113.10 4.52 0.50 N 32 1 C8 B DG 18 ? ? N9 B DG 18 ? ? C4 B DG 18 ? ? 103.69 106.40 -2.71 0.40 N 33 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 110.65 108.30 2.35 0.30 N 34 1 "O4'" B DC 20 ? ? "C1'" B DC 20 ? ? N1 B DC 20 ? ? 111.31 108.30 3.01 0.30 N 35 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 111.57 108.30 3.27 0.30 N 36 1 N7 B DG 22 ? ? C8 B DG 22 ? ? N9 B DG 22 ? ? 117.81 113.10 4.71 0.50 N 37 1 C8 B DG 22 ? ? N9 B DG 22 ? ? C4 B DG 22 ? ? 103.98 106.40 -2.42 0.40 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1DJD 'double helix' 1DJD '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 11 1_555 0.173 -0.126 0.036 -6.085 -6.767 -0.142 1 A_DC1:DG22_B A 1 ? B 22 ? 19 1 1 A DG 2 1_555 B DC 10 1_555 -0.124 -0.108 0.208 10.110 -2.142 -3.796 2 A_DG2:DC21_B A 2 ? B 21 ? 19 1 1 A DG 3 1_555 B DC 9 1_555 -0.198 -0.072 0.103 16.065 -7.424 -0.594 3 A_DG3:DC20_B A 3 ? B 20 ? 19 1 1 A DA 4 1_555 B DT 8 1_555 0.131 -0.129 0.078 -3.027 -4.077 1.149 4 A_DA4:DT19_B A 4 ? B 19 ? 20 1 1 A DC 5 1_555 B DG 7 1_555 0.177 -0.105 0.477 17.830 6.796 1.855 5 A_DC5:DG18_B A 5 ? B 18 ? 19 1 1 A DA 6 1_555 B DT 6 1_555 2.729 0.822 0.572 -24.992 24.351 -43.998 6 A_DA6:DT17_B A 6 ? B 17 ? ? ? 1 A DA 7 1_555 B DT 5 1_555 0.243 0.063 0.675 7.687 -2.553 -2.788 7 A_DA7:DT16_B A 7 ? B 16 ? 20 1 1 A DG 8 1_555 B DC 4 1_555 -0.143 -0.123 0.074 7.594 -5.843 -3.364 8 A_DG8:DC15_B A 8 ? B 15 ? 19 1 1 A DA 9 1_555 B DT 3 1_555 0.127 -0.076 -0.016 12.324 -9.549 0.767 9 A_DA9:DT14_B A 9 ? B 14 ? 20 1 1 A DA 10 1_555 B DT 2 1_555 0.098 -0.099 -0.074 10.109 -9.671 4.197 10 A_DA10:DT13_B A 10 ? B 13 ? 20 1 1 A DG 11 1_555 B DC 1 1_555 -0.139 -0.110 0.260 18.448 -1.954 -2.985 11 A_DG11:DC12_B A 11 ? B 12 ? 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 11 1_555 A DG 2 1_555 B DC 10 1_555 -0.316 -0.365 2.725 0.172 9.561 27.979 -2.374 0.651 2.467 19.082 -0.343 29.538 1 AA_DC1DG2:DC21DG22_BB A 1 ? B 22 ? A 2 ? B 21 ? 1 A DG 2 1_555 B DC 10 1_555 A DG 3 1_555 B DC 9 1_555 0.688 -0.057 3.142 0.511 0.761 37.434 -0.185 -1.008 3.149 1.185 -0.796 37.445 2 AA_DG2DG3:DC20DC21_BB A 2 ? B 21 ? A 3 ? B 20 ? 1 A DG 3 1_555 B DC 9 1_555 A DA 4 1_555 B DT 8 1_555 0.276 0.299 4.282 1.416 8.186 38.317 -0.849 -0.188 4.262 12.296 -2.127 39.174 3 AA_DG3DA4:DT19DC20_BB A 3 ? B 20 ? A 4 ? B 19 ? 1 A DA 4 1_555 B DT 8 1_555 A DC 5 1_555 B DG 7 1_555 -0.082 -0.041 3.178 1.393 1.327 32.402 -0.299 0.384 3.168 2.375 -2.494 32.458 4 AA_DA4DC5:DG18DT19_BB A 4 ? B 19 ? A 5 ? B 18 ? 1 A DA 6 1_555 B DT 6 1_555 A DA 7 1_555 B DT 5 1_555 2.431 -0.577 2.906 -6.770 -3.979 17.684 -0.183 -9.849 1.933 -12.191 20.745 19.336 5 AA_DA6DA7:DT16DT17_BB A 6 ? B 17 ? A 7 ? B 16 ? 1 A DA 7 1_555 B DT 5 1_555 A DG 8 1_555 B DC 4 1_555 -0.186 -0.661 3.443 1.375 3.221 32.198 -1.776 0.587 3.352 5.787 -2.470 32.383 6 AA_DA7DG8:DC15DT16_BB A 7 ? B 16 ? A 8 ? B 15 ? 1 A DG 8 1_555 B DC 4 1_555 A DA 9 1_555 B DT 3 1_555 -0.139 -0.344 3.192 -0.103 2.597 35.428 -0.932 0.214 3.160 4.260 0.169 35.520 7 AA_DG8DA9:DT14DC15_BB A 8 ? B 15 ? A 9 ? B 14 ? 1 A DA 9 1_555 B DT 3 1_555 A DA 10 1_555 B DT 2 1_555 -0.217 -0.580 3.225 0.846 7.227 33.836 -2.055 0.491 3.034 12.241 -1.433 34.587 8 AA_DA9DA10:DT13DT14_BB A 9 ? B 14 ? A 10 ? B 13 ? 1 A DA 10 1_555 B DT 2 1_555 A DG 11 1_555 B DC 1 1_555 -0.081 -0.146 2.988 -0.496 0.195 30.048 -0.317 0.063 2.988 0.376 0.956 30.052 9 AA_DA10DG11:DC12DT13_BB A 10 ? B 13 ? A 11 ? B 12 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name '8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL' _pdbx_entity_nonpoly.comp_id TBT #