data_1DXA # _entry.id 1DXA # _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 1DXA pdb_00001dxa 10.2210/pdb1dxa/pdb WWPDB D_1000172955 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DXA _pdbx_database_status.recvd_initial_deposition_date 1995-09-01 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yeh, H.J.C.' 1 'Sayer, J.M.' 2 'Liu, X.' 3 'Altieri, A.S.' 4 'Byrd, R.A.' 5 'Lakshman, M.K.' 6 'Yagi, H.' 7 'Schurter, E.J.' 8 'Gorenstein, D.G.' 9 'Jerina, D.M.' 10 # _citation.id primary _citation.title ;NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene: an unusual syn glycosidic torsion angle at the modified dA ; _citation.journal_abbrev Biochemistry _citation.journal_volume 34 _citation.page_first 13570 _citation.page_last 13581 _citation.year 1995 _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 7577946 _citation.pdbx_database_id_DOI 10.1021/bi00041a037 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yeh, H.J.' 1 ? primary 'Sayer, J.M.' 2 ? primary 'Liu, X.' 3 ? primary 'Altieri, A.S.' 4 ? primary 'Byrd, R.A.' 5 ? primary 'Lakshman, M.K.' 6 ? primary 'Yagi, H.' 7 ? primary 'Schurter, E.J.' 8 ? primary 'Gorenstein, D.G.' 9 ? primary 'Jerina, D.M.' 10 ? # _cell.entry_id 1DXA _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 1DXA _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(*GP*GP*TP*CP*AP*CP*GP*AP*G)-3') ; 2780.836 1 ? ? ? 'BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA' 2 polymer syn ;DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3') ; 2716.787 1 ? ? ? 'BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA' 3 non-polymer syn '1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE' 304.339 1 ? ? ? ? # loop_ _entity_keywords.entity_id _entity_keywords.text 1 'DEOXYRIBONUCLEIC ACID' 2 'DEOXYRIBONUCLEIC ACID' # 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 '(DG)(DG)(DT)(DC)(DA)(DC)(DG)(DA)(DG)' GGTCACGAG A ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DC)(DG)(DG)(DG)(DA)(DC)(DC)' CTCGGGACC B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DG n 1 3 DT n 1 4 DC n 1 5 DA n 1 6 DC n 1 7 DG n 1 8 DA n 1 9 DG n 2 1 DC n 2 2 DT n 2 3 DC n 2 4 DG n 2 5 DG n 2 6 DG n 2 7 DA n 2 8 DC n 2 9 DC n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'chemically synthesized' 2 1 sample ? ? ? ? ? 'chemically synthesized' 3 1 sample ? ? ? ? ? 'chemically synthesized' # 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 1DXA 1DXA ? ? ? 2 2 PDB 1DXA 1DXA ? ? ? # 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 1DXA A 1 ? 9 ? 1DXA 1 ? 9 ? 1 9 2 2 1DXA B 1 ? 9 ? 1DXA 1 ? 9 ? 1 9 # 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 BAP non-polymer . '1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE' ? 'C20 H16 O3' 304.339 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 # _pdbx_nmr_refine.entry_id 1DXA _pdbx_nmr_refine.method 'ENERGY MINIMIZATION, MOLECULAR DYNAMICS' _pdbx_nmr_refine.details ;TWO STARTING STRUCTURES WITH BENZO[A]PYRENE MOIETY INSIDE THE DUPLEX AND OUTSIDE THE DUPLEX, RESPECTIVELY, WERE GENERATED BY CONNECTING A STANDARD B-TYPE DNA FRAGMENT WITH A MANUALLY BUILD (+)-DE2-[BAP] FRAGMENT. SOLUTION STRUCTURES FOR THE DUPLEX WERE GENERATED BY RESTRAINTED MOLECULAR DYNAMICS AND RESTRAINTED ENERGY MINIMIZATION USING A SET OF INTER-PROTON DISTANCE RESTRAINTS AND DIHEDRAL ANGLE RESTRAINTS WHICH WERE DERIVED FROM NMR EXPERIMENTS. SOME OF STRUCTURES WITH MINIMUM RESTRAINT VIOLATIONS WERE FURTHER REFINED BY THE ITERATIVE RELAXATION MATRIX ANALYSIS (IRMA) METHOD OVER 111 WELL-SEPARATED CROSS PEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 50, 80, 120, 160 AND 200 MS. THE STRUCTURE PRESENTED HERE WAS ONE OF THE FIVE REFINED AND MINIMIZED STRUCTURES. THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS. THESE WERE; (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM NOE DATA; (2) BACKBONE DIHEDRAL ANGLE RESTRAINTS FOR A STANDARD B-DNA EXCEPT THOSE IMMEDIATELY ADJACENT TO THE MODIFIED RESIDUE; (3) DIHEDRAL ANGLE RESTRAINTS FOR ALL GLYCOSIDIC BONDS, EXCEPT MODIFIED DA RESIDUE IN THE CENTER; (4) HYDROGEN BOND RESTRAINTS (BOTH DISTANCE AND PLANARITY ) FOR ALL BASE-PAIRS EXCEPT CENTRAL DA-DG MISMATCH PAIR. THESE RESTRAINTS WERE JUSTIFIED BY THE FACT THAT THE MODIFIED DUPLEX DISPLAYED CHARACTERISTIC NMR SPECTRA OF A B-DNA EXCEPT NEAR LESION SITE, WHERE THE BAP MOIETY WAS INTERCALATED. THE MODIFIED DA RESIDUE DISPLAYED C3'-ENDO SUGAR RING AND A SYN GLYCOSIDIC BOND. IT ALSO FORMED A NON-WATSON-CRICK BASE PAIR WITH THE OPPOSITE DG. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1DXA _pdbx_nmr_details.text ;(+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH TRANS ADDITION AT THE C10 OF THE EPOXIDE. ; # _pdbx_nmr_ensemble.entry_id 1DXA _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? _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_software.name NMRCHITECT _pdbx_nmr_software.version ? _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors BIOSYM _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 1DXA _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1DXA _struct.title 'BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DXA _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DOUBLE HELIX, BENZO[A]PYRENE DIOL EPOXIDE ADDUCT, DUPLEX DNA, NON-WATSON-CRICK BASE PAIR, 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 5 N6 ? ? ? 1_555 C BAP . "C4'" ? ? A DA 5 A BAP 10 1_555 ? ? ? ? ? ? ? 1.470 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 1 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 1 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 1 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 2 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 2 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 2 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 3 B DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 3 B DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 4 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 4 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 4 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DG 5 O6 ? ? A DA 5 B DG 5 1_555 ? ? ? ? ? ? TYPE_9_PAIR ? ? ? hydrog13 hydrog ? ? A DA 5 N7 ? ? ? 1_555 B DG 5 N1 ? ? A DA 5 B DG 5 1_555 ? ? ? ? ? ? TYPE_9_PAIR ? ? ? hydrog14 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 6 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 6 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 6 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 7 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 7 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 7 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 8 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 8 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 9 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 9 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 9 B DC 1 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 BAP _struct_site.pdbx_auth_seq_id 10 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE BAP A 10' # 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 4 DA A 5 ? DA A 5 . ? 1_555 ? 2 AC1 4 DC A 6 ? DC A 6 . ? 1_555 ? 3 AC1 4 DG B 4 ? DG B 4 . ? 1_555 ? 4 AC1 4 DG B 5 ? DG B 5 . ? 1_555 ? # _database_PDB_matrix.entry_id 1DXA _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 1DXA _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 DG 1 1 1 DG G A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DG 9 9 9 DG G A . n B 2 1 DC 1 1 1 DC C B . n B 2 2 DT 2 2 2 DT T B . n B 2 3 DC 3 3 3 DC C B . n B 2 4 DG 4 4 4 DG G B . n B 2 5 DG 5 5 5 DG G B . n B 2 6 DG 6 6 6 DG G B . n B 2 7 DA 7 7 7 DA A B . n B 2 8 DC 8 8 8 DC C B . n B 2 9 DC 9 9 9 DC C B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id BAP _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 10 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id BAP _pdbx_nonpoly_scheme.auth_mon_id BAP _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 1995-12-07 2 'Structure model' 1 1 2008-03-24 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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 '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' database_2 2 4 'Structure model' pdbx_database_status 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_database_status.process_site' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 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 DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 110.79 108.30 2.49 0.30 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.52 108.30 4.22 0.30 N 3 1 "C3'" A DA 5 ? ? "C2'" A DA 5 ? ? "C1'" A DA 5 ? ? 96.36 102.40 -6.04 0.80 N 4 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 112.52 108.30 4.22 0.30 N 5 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 112.56 108.30 4.26 0.30 N 6 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 110.36 108.30 2.06 0.30 N 7 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 112.17 108.30 3.87 0.30 N 8 1 "C3'" B DC 1 ? ? "C2'" B DC 1 ? ? "C1'" B DC 1 ? ? 97.28 102.40 -5.12 0.80 N 9 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 113.47 108.30 5.17 0.30 N 10 1 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 111.22 108.30 2.92 0.30 N 11 1 "O4'" B DG 4 ? ? "C1'" B DG 4 ? ? N9 B DG 4 ? ? 110.24 108.30 1.94 0.30 N 12 1 "O4'" B DG 5 ? ? "C1'" B DG 5 ? ? N9 B DG 5 ? ? 111.67 108.30 3.37 0.30 N 13 1 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? N9 B DG 6 ? ? 111.67 108.30 3.36 0.30 N 14 1 "O4'" B DA 7 ? ? "C1'" B DA 7 ? ? N9 B DA 7 ? ? 111.21 108.30 2.91 0.30 N 15 1 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 110.67 108.30 2.37 0.30 N 16 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 110.59 108.30 2.29 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DG A 2 ? ? 0.096 'SIDE CHAIN' 2 1 DT A 3 ? ? 0.132 'SIDE CHAIN' 3 1 DA A 5 ? ? 0.082 'SIDE CHAIN' 4 1 DA A 8 ? ? 0.072 'SIDE CHAIN' 5 1 DT B 2 ? ? 0.115 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1DXA 'double helix' 1DXA 'b-form double helix' 1DXA 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 B DC 9 1_555 -0.950 -0.293 0.123 8.126 -5.923 -1.433 1 A_DG1:DC9_B A 1 ? B 9 ? 19 1 1 A DG 2 1_555 B DC 8 1_555 -1.004 -0.354 0.001 -2.005 -10.092 -1.499 2 A_DG2:DC8_B A 2 ? B 8 ? 19 1 1 A DT 3 1_555 B DA 7 1_555 0.402 -0.104 -0.015 5.711 -8.808 1.754 3 A_DT3:DA7_B A 3 ? B 7 ? 20 1 1 A DC 4 1_555 B DG 6 1_555 0.730 -0.217 0.226 5.815 -7.584 -1.811 4 A_DC4:DG6_B A 4 ? B 6 ? 19 1 1 A DA 5 1_555 B DG 5 1_555 -0.021 -4.454 -1.217 41.195 21.481 90.797 5 A_DA5:DG5_B A 5 ? B 5 ? 9 ? 1 A DC 6 1_555 B DG 4 1_555 0.560 -0.086 0.661 -26.293 2.338 -2.966 6 A_DC6:DG4_B A 6 ? B 4 ? 19 1 1 A DG 7 1_555 B DC 3 1_555 -1.226 -0.301 0.223 10.862 -5.893 3.263 7 A_DG7:DC3_B A 7 ? B 3 ? 19 1 1 A DA 8 1_555 B DT 2 1_555 -0.505 -0.145 -0.130 7.669 -13.597 4.234 8 A_DA8:DT2_B A 8 ? B 2 ? 20 1 1 A DG 9 1_555 B DC 1 1_555 0.195 -0.024 -0.174 1.349 -8.773 -2.969 9 A_DG9:DC1_B A 9 ? 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 DG 1 1_555 B DC 9 1_555 A DG 2 1_555 B DC 8 1_555 0.033 -0.951 3.373 1.027 -0.106 39.694 -1.388 0.075 3.375 -0.157 -1.512 39.707 1 AA_DG1DG2:DC8DC9_BB A 1 ? B 9 ? A 2 ? B 8 ? 1 A DG 2 1_555 B DC 8 1_555 A DT 3 1_555 B DA 7 1_555 0.024 -0.509 2.990 0.263 3.257 41.789 -1.020 -0.008 2.944 4.558 -0.368 41.911 2 AA_DG2DT3:DA7DC8_BB A 2 ? B 8 ? A 3 ? B 7 ? 1 A DT 3 1_555 B DA 7 1_555 A DC 4 1_555 B DG 6 1_555 0.560 -0.376 3.150 -1.244 5.186 33.373 -1.446 -1.154 3.036 8.960 2.149 33.785 3 AA_DT3DC4:DG6DA7_BB A 3 ? B 7 ? A 4 ? B 6 ? 1 A DC 4 1_555 B DG 6 1_555 A DA 5 1_555 B DG 5 1_555 -0.267 -3.791 2.146 -169.400 18.315 2.982 -2.011 -0.867 -0.086 9.661 89.354 170.390 4 AA_DC4DA5:DG5DG6_BB A 4 ? B 6 ? A 5 ? B 5 ? 1 A DA 5 1_555 B DG 5 1_555 A DC 6 1_555 B DG 4 1_555 -1.494 -5.703 -1.793 127.489 -80.862 76.680 -3.108 0.447 0.254 -43.319 -68.297 157.326 5 AA_DA5DC6:DG4DG5_BB A 5 ? B 5 ? A 6 ? B 4 ? 1 A DC 6 1_555 B DG 4 1_555 A DG 7 1_555 B DC 3 1_555 -0.783 -0.554 2.267 0.705 1.310 26.607 -1.437 1.825 2.216 2.844 -1.530 26.648 6 AA_DC6DG7:DC3DG4_BB A 6 ? B 4 ? A 7 ? B 3 ? 1 A DG 7 1_555 B DC 3 1_555 A DA 8 1_555 B DT 2 1_555 -0.259 -0.387 3.247 2.493 2.155 36.957 -0.893 0.736 3.197 3.392 -3.923 37.098 7 AA_DG7DA8:DT2DC3_BB A 7 ? B 3 ? A 8 ? B 2 ? 1 A DA 8 1_555 B DT 2 1_555 A DG 9 1_555 B DC 1 1_555 0.361 -0.851 3.325 -0.147 4.837 38.043 -1.901 -0.567 3.196 7.384 0.224 38.338 8 AA_DA8DG9:DC1DT2_BB A 8 ? B 2 ? A 9 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name '1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE' _pdbx_entity_nonpoly.comp_id BAP #