data_2KAR # _entry.id 2KAR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2KAR pdb_00002kar 10.2210/pdb2kar/pdb RCSB RCSB100889 ? ? WWPDB D_1000100889 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2KAS _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KAR _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-11-13 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _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 'Huang, H.' 1 'Wang, H.' 2 'Lloyd, R.S.' 3 'Rizzo, C.J.' 4 'Stone, M.P.' 5 # _citation.id primary _citation.title ;Conformational interconversion of the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N(2)-deoxyguanosine adduct when mismatched with deoxyadenosine in DNA ; _citation.journal_abbrev Chem.Res.Toxicol. _citation.journal_volume 22 _citation.page_first 187 _citation.page_last 200 _citation.year 2009 _citation.journal_id_ASTM CRTOEC _citation.country US _citation.journal_id_ISSN 0893-228X _citation.journal_id_CSD 2140 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19053179 _citation.pdbx_database_id_DOI 10.1021/tx800320m # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Huang, H.' 1 ? primary 'Wang, H.' 2 ? primary 'Lloyd, R.S.' 3 ? primary 'Rizzo, C.J.' 4 ? primary 'Stone, M.P.' 5 ? # 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 "5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'" 3663.392 1 ? ? ? ? 2 polymer syn "5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3'" 3687.417 1 ? ? ? ? 3 non-polymer syn '(4S)-nonane-1,4-diol' 160.254 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 '(DG)(DC)(DT)(DA)(DG)(DC)(DG)(DA)(DG)(DT)(DC)(DC)' GCTAGCGAGTCC A ? 2 polydeoxyribonucleotide no no '(DG)(DG)(DA)(DC)(DT)(DA)(DG)(DC)(DT)(DA)(DG)(DC)' GGACTAGCTAGC 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 DC n 1 3 DT n 1 4 DA n 1 5 DG n 1 6 DC n 1 7 DG n 1 8 DA n 1 9 DG n 1 10 DT n 1 11 DC n 1 12 DC n 2 1 DG n 2 2 DG n 2 3 DA n 2 4 DC n 2 5 DT n 2 6 DA n 2 7 DG n 2 8 DC n 2 9 DT n 2 10 DA n 2 11 DG n 2 12 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 ? ? ? ? ? 'The DNA oligomer is chemically synthesized.' 2 1 sample ? ? ? ? ? 'The DNA oligomer is chemically synthesized.' # 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 2KAR 2KAR 1 1 GCTAGCGAGTCC ? 2 PDB 2KAR 2KAR 2 1 GGACTAGCTAGC ? # 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 2KAR A 1 ? 12 ? 2KAR 1 ? 12 ? 1 12 2 2 2KAR B 1 ? 12 ? 2KAR 13 ? 24 ? 13 24 # 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 HND non-polymer . '(4S)-nonane-1,4-diol' ? 'C9 H20 O2' 160.254 # _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.solution_id 1 _pdbx_nmr_exptl.type '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 100 _pdbx_nmr_exptl_sample_conditions.pH 5.5 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 288 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents ;1.0 mM DNA 5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3', 1.0 mM 5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3', 1.0 mM (2E,4R)-4-HYDROXYNON-2-ENAL, 90% H2O/10% D2O ; _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2KAR _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'back calculated data agree with experimental NOESY spectrum' _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KAR _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2KAR _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_software.authors 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name Amber _pdbx_nmr_software.version ? _pdbx_nmr_software.ordinal 1 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KAR _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KAR _struct.title 'HNE-dG adduct mismatched with dA in acidic solution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KAR _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'HNE-dG, mismatch, hydroxynonenal, 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 _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 covale1 covale one ? A DG 7 N2 ? ? ? 1_555 C HND . C3 ? ? A DG 7 A HND 25 1_555 ? ? ? ? ? ? ? 1.457 ? ? covale2 covale one ? A DG 7 N1 ? ? ? 1_555 C HND . C1 ? ? A DG 7 A HND 25 1_555 ? ? ? ? ? ? ? 1.487 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 12 N3 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 12 O2 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 12 N4 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 10 N6 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DA 6 N6 ? ? A DG 7 B DA 18 1_555 ? ? ? ? ? ? 'DG-DA MISPAIR' ? ? ? hydrog18 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 12 B DG 13 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 HND _struct_site.pdbx_auth_seq_id 25 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE HND 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 4 DG A 5 ? DG A 5 . ? 1_555 ? 2 AC1 4 DC A 6 ? DC A 6 . ? 1_555 ? 3 AC1 4 DG A 7 ? DG A 7 . ? 1_555 ? 4 AC1 4 DC B 4 ? DC B 16 . ? 1_555 ? # _atom_sites.entry_id 2KAR _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 DG A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DC 12 12 12 DC DC A . n B 2 1 DG 1 13 13 DG DG B . n B 2 2 DG 2 14 14 DG DG B . n B 2 3 DA 3 15 15 DA DA B . n B 2 4 DC 4 16 16 DC DC B . n B 2 5 DT 5 17 17 DT DT B . n B 2 6 DA 6 18 18 DA DA B . n B 2 7 DG 7 19 19 DG DG B . n B 2 8 DC 8 20 20 DC DC B . n B 2 9 DT 9 21 21 DT DT B . n B 2 10 DA 10 22 22 DA DA B . n B 2 11 DG 11 23 23 DG DG B . n B 2 12 DC 12 24 24 DC DC B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id HND _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 25 _pdbx_nonpoly_scheme.auth_seq_num 25 _pdbx_nonpoly_scheme.pdb_mon_id HND _pdbx_nonpoly_scheme.auth_mon_id HND _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 2009-05-26 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' database_2 2 3 'Structure model' pdbx_nmr_software 3 3 'Structure model' pdbx_nmr_spectrometer 4 3 'Structure model' pdbx_struct_assembly 5 3 'Structure model' pdbx_struct_oper_list 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_nmr_software.name' 4 3 'Structure model' '_pdbx_nmr_spectrometer.model' 5 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 7 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 8 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_entry_details.entry_id 2KAR _pdbx_entry_details.nonpolymer_details ;THE LIGAND HND FORMS TWO COVALENT BONDS WITH THE DEOXY-GUANINE AT POSITION 7 OF CHAIN A. THIS LIGAND IS FORMED BY CHEMICAL REACTION OF ANOTHER LIGAND HNE ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_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 C2 A DG 1 ? ? N3 A DG 1 ? ? 1.385 1.323 0.062 0.008 N 2 1 N3 A DG 1 ? ? C4 A DG 1 ? ? 1.414 1.350 0.064 0.007 N 3 1 N7 A DG 1 ? ? C8 A DG 1 ? ? 1.405 1.305 0.100 0.006 N 4 1 N1 A DA 4 ? ? C2 A DA 4 ? ? 1.410 1.339 0.071 0.009 N 5 1 C2 A DA 4 ? ? N3 A DA 4 ? ? 1.408 1.331 0.077 0.009 N 6 1 N3 A DA 4 ? ? C4 A DA 4 ? ? 1.407 1.344 0.063 0.006 N 7 1 C6 A DA 4 ? ? N1 A DA 4 ? ? 1.397 1.351 0.046 0.007 N 8 1 N7 A DA 4 ? ? C8 A DA 4 ? ? 1.412 1.311 0.101 0.007 N 9 1 C2 A DG 5 ? ? N3 A DG 5 ? ? 1.387 1.323 0.064 0.008 N 10 1 N3 A DG 5 ? ? C4 A DG 5 ? ? 1.413 1.350 0.063 0.007 N 11 1 N7 A DG 5 ? ? C8 A DG 5 ? ? 1.404 1.305 0.099 0.006 N 12 1 C2 A DG 7 ? ? N3 A DG 7 ? ? 1.388 1.323 0.065 0.008 N 13 1 N3 A DG 7 ? ? C4 A DG 7 ? ? 1.408 1.350 0.058 0.007 N 14 1 N7 A DG 7 ? ? C8 A DG 7 ? ? 1.400 1.305 0.095 0.006 N 15 1 N1 A DA 8 ? ? C2 A DA 8 ? ? 1.409 1.339 0.070 0.009 N 16 1 C2 A DA 8 ? ? N3 A DA 8 ? ? 1.407 1.331 0.076 0.009 N 17 1 N3 A DA 8 ? ? C4 A DA 8 ? ? 1.406 1.344 0.062 0.006 N 18 1 C6 A DA 8 ? ? N1 A DA 8 ? ? 1.394 1.351 0.043 0.007 N 19 1 N7 A DA 8 ? ? C8 A DA 8 ? ? 1.412 1.311 0.101 0.007 N 20 1 C2 A DG 9 ? ? N3 A DG 9 ? ? 1.387 1.323 0.064 0.008 N 21 1 N3 A DG 9 ? ? C4 A DG 9 ? ? 1.413 1.350 0.063 0.007 N 22 1 N7 A DG 9 ? ? C8 A DG 9 ? ? 1.402 1.305 0.097 0.006 N 23 1 C2 B DG 13 ? ? N3 B DG 13 ? ? 1.386 1.323 0.063 0.008 N 24 1 N3 B DG 13 ? ? C4 B DG 13 ? ? 1.415 1.350 0.065 0.007 N 25 1 N7 B DG 13 ? ? C8 B DG 13 ? ? 1.405 1.305 0.100 0.006 N 26 1 C2 B DG 14 ? ? N3 B DG 14 ? ? 1.386 1.323 0.063 0.008 N 27 1 N3 B DG 14 ? ? C4 B DG 14 ? ? 1.413 1.350 0.063 0.007 N 28 1 N7 B DG 14 ? ? C8 B DG 14 ? ? 1.406 1.305 0.101 0.006 N 29 1 N1 B DA 15 ? ? C2 B DA 15 ? ? 1.410 1.339 0.071 0.009 N 30 1 C2 B DA 15 ? ? N3 B DA 15 ? ? 1.411 1.331 0.080 0.009 N 31 1 N3 B DA 15 ? ? C4 B DA 15 ? ? 1.405 1.344 0.061 0.006 N 32 1 N7 B DA 15 ? ? C8 B DA 15 ? ? 1.409 1.311 0.098 0.007 N 33 1 N1 B DA 18 ? ? C2 B DA 18 ? ? 1.407 1.339 0.068 0.009 N 34 1 C2 B DA 18 ? ? N3 B DA 18 ? ? 1.404 1.331 0.073 0.009 N 35 1 N3 B DA 18 ? ? C4 B DA 18 ? ? 1.402 1.344 0.058 0.006 N 36 1 N7 B DA 18 ? ? C8 B DA 18 ? ? 1.412 1.311 0.101 0.007 N 37 1 C6 B DA 18 ? ? N6 B DA 18 ? ? 1.388 1.335 0.053 0.008 N 38 1 C2 B DG 19 ? ? N3 B DG 19 ? ? 1.383 1.323 0.060 0.008 N 39 1 N3 B DG 19 ? ? C4 B DG 19 ? ? 1.411 1.350 0.061 0.007 N 40 1 N7 B DG 19 ? ? C8 B DG 19 ? ? 1.406 1.305 0.101 0.006 N 41 1 N1 B DA 22 ? ? C2 B DA 22 ? ? 1.410 1.339 0.071 0.009 N 42 1 C2 B DA 22 ? ? N3 B DA 22 ? ? 1.407 1.331 0.076 0.009 N 43 1 N3 B DA 22 ? ? C4 B DA 22 ? ? 1.406 1.344 0.062 0.006 N 44 1 C6 B DA 22 ? ? N1 B DA 22 ? ? 1.395 1.351 0.044 0.007 N 45 1 N7 B DA 22 ? ? C8 B DA 22 ? ? 1.412 1.311 0.101 0.007 N 46 1 C2 B DG 23 ? ? N3 B DG 23 ? ? 1.386 1.323 0.063 0.008 N 47 1 N3 B DG 23 ? ? C4 B DG 23 ? ? 1.413 1.350 0.063 0.007 N 48 1 N7 B DG 23 ? ? C8 B DG 23 ? ? 1.406 1.305 0.101 0.006 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 DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 110.21 108.30 1.91 0.30 N 2 1 N3 A DG 1 ? ? C4 A DG 1 ? ? C5 A DG 1 ? ? 125.24 128.60 -3.36 0.50 N 3 1 N9 A DG 1 ? ? C4 A DG 1 ? ? C5 A DG 1 ? ? 108.90 105.40 3.50 0.40 N 4 1 OP1 A DC 2 ? ? P A DC 2 ? ? OP2 A DC 2 ? ? 105.38 119.60 -14.22 1.50 N 5 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.52 108.30 2.22 0.30 N 6 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 122.78 118.90 3.88 0.60 N 7 1 N3 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 116.09 121.90 -5.81 0.70 N 8 1 OP1 A DT 3 ? ? P A DT 3 ? ? OP2 A DT 3 ? ? 105.26 119.60 -14.34 1.50 N 9 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.45 108.30 2.15 0.30 N 10 1 N3 A DT 3 ? ? C2 A DT 3 ? ? O2 A DT 3 ? ? 118.42 122.30 -3.88 0.60 N 11 1 OP1 A DA 4 ? ? P A DA 4 ? ? OP2 A DA 4 ? ? 105.04 119.60 -14.56 1.50 N 12 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.06 108.30 2.76 0.30 N 13 1 N1 A DA 4 ? ? C2 A DA 4 ? ? N3 A DA 4 ? ? 124.52 129.30 -4.78 0.50 N 14 1 C2 A DA 4 ? ? N3 A DA 4 ? ? C4 A DA 4 ? ? 114.47 110.60 3.87 0.50 N 15 1 C5 A DA 4 ? ? C6 A DA 4 ? ? N1 A DA 4 ? ? 122.82 117.70 5.12 0.50 N 16 1 C5 A DA 4 ? ? N7 A DA 4 ? ? C8 A DA 4 ? ? 100.54 103.90 -3.36 0.50 N 17 1 OP1 A DG 5 ? ? P A DG 5 ? ? OP2 A DG 5 ? ? 105.21 119.60 -14.39 1.50 N 18 1 N3 A DG 5 ? ? C4 A DG 5 ? ? C5 A DG 5 ? ? 125.56 128.60 -3.04 0.50 N 19 1 N9 A DG 5 ? ? C4 A DG 5 ? ? C5 A DG 5 ? ? 108.67 105.40 3.27 0.40 N 20 1 OP1 A DC 6 ? ? P A DC 6 ? ? OP2 A DC 6 ? ? 105.55 119.60 -14.05 1.50 N 21 1 N3 A DC 6 ? ? C2 A DC 6 ? ? O2 A DC 6 ? ? 116.09 121.90 -5.81 0.70 N 22 1 OP1 A DG 7 ? ? P A DG 7 ? ? OP2 A DG 7 ? ? 104.89 119.60 -14.71 1.50 N 23 1 N3 A DG 7 ? ? C4 A DG 7 ? ? C5 A DG 7 ? ? 124.28 128.60 -4.32 0.50 N 24 1 N9 A DG 7 ? ? C4 A DG 7 ? ? C5 A DG 7 ? ? 108.17 105.40 2.77 0.40 N 25 1 N3 A DG 7 ? ? C2 A DG 7 ? ? N2 A DG 7 ? ? 114.82 119.90 -5.08 0.70 N 26 1 OP1 A DA 8 ? ? P A DA 8 ? ? OP2 A DA 8 ? ? 106.01 119.60 -13.59 1.50 N 27 1 N1 A DA 8 ? ? C2 A DA 8 ? ? N3 A DA 8 ? ? 124.37 129.30 -4.93 0.50 N 28 1 C2 A DA 8 ? ? N3 A DA 8 ? ? C4 A DA 8 ? ? 114.57 110.60 3.97 0.50 N 29 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N1 A DA 8 ? ? 122.58 117.70 4.88 0.50 N 30 1 C5 A DA 8 ? ? N7 A DA 8 ? ? C8 A DA 8 ? ? 100.70 103.90 -3.20 0.50 N 31 1 N1 A DA 8 ? ? C6 A DA 8 ? ? N6 A DA 8 ? ? 114.86 118.60 -3.74 0.60 N 32 1 OP1 A DG 9 ? ? P A DG 9 ? ? OP2 A DG 9 ? ? 105.04 119.60 -14.56 1.50 N 33 1 N3 A DG 9 ? ? C4 A DG 9 ? ? C5 A DG 9 ? ? 125.34 128.60 -3.26 0.50 N 34 1 N9 A DG 9 ? ? C4 A DG 9 ? ? C5 A DG 9 ? ? 108.39 105.40 2.99 0.40 N 35 1 OP1 A DT 10 ? ? P A DT 10 ? ? OP2 A DT 10 ? ? 105.21 119.60 -14.39 1.50 N 36 1 "O4'" A DT 10 ? ? "C1'" A DT 10 ? ? N1 A DT 10 ? ? 110.49 108.30 2.19 0.30 N 37 1 N3 A DT 10 ? ? C2 A DT 10 ? ? O2 A DT 10 ? ? 118.37 122.30 -3.93 0.60 N 38 1 OP1 A DC 11 ? ? P A DC 11 ? ? OP2 A DC 11 ? ? 105.68 119.60 -13.92 1.50 N 39 1 N1 A DC 11 ? ? C2 A DC 11 ? ? O2 A DC 11 ? ? 122.87 118.90 3.97 0.60 N 40 1 N3 A DC 11 ? ? C2 A DC 11 ? ? O2 A DC 11 ? ? 116.05 121.90 -5.85 0.70 N 41 1 OP1 A DC 12 ? ? P A DC 12 ? ? OP2 A DC 12 ? ? 105.02 119.60 -14.58 1.50 N 42 1 "O4'" A DC 12 ? ? "C1'" A DC 12 ? ? N1 A DC 12 ? ? 113.56 108.30 5.26 0.30 N 43 1 N1 A DC 12 ? ? C2 A DC 12 ? ? O2 A DC 12 ? ? 122.93 118.90 4.03 0.60 N 44 1 N3 A DC 12 ? ? C2 A DC 12 ? ? O2 A DC 12 ? ? 115.82 121.90 -6.08 0.70 N 45 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 110.30 108.30 2.00 0.30 N 46 1 N3 B DG 13 ? ? C4 B DG 13 ? ? C5 B DG 13 ? ? 125.36 128.60 -3.24 0.50 N 47 1 N9 B DG 13 ? ? C4 B DG 13 ? ? C5 B DG 13 ? ? 108.51 105.40 3.11 0.40 N 48 1 OP1 B DG 14 ? ? P B DG 14 ? ? OP2 B DG 14 ? ? 105.05 119.60 -14.55 1.50 N 49 1 N3 B DG 14 ? ? C4 B DG 14 ? ? C5 B DG 14 ? ? 125.59 128.60 -3.01 0.50 N 50 1 N9 B DG 14 ? ? C4 B DG 14 ? ? C5 B DG 14 ? ? 108.63 105.40 3.23 0.40 N 51 1 OP1 B DA 15 ? ? P B DA 15 ? ? OP2 B DA 15 ? ? 105.28 119.60 -14.32 1.50 N 52 1 N1 B DA 15 ? ? C2 B DA 15 ? ? N3 B DA 15 ? ? 124.51 129.30 -4.79 0.50 N 53 1 C2 B DA 15 ? ? N3 B DA 15 ? ? C4 B DA 15 ? ? 114.56 110.60 3.96 0.50 N 54 1 C5 B DA 15 ? ? C6 B DA 15 ? ? N1 B DA 15 ? ? 122.84 117.70 5.14 0.50 N 55 1 C5 B DA 15 ? ? N7 B DA 15 ? ? C8 B DA 15 ? ? 100.42 103.90 -3.48 0.50 N 56 1 OP1 B DC 16 ? ? P B DC 16 ? ? OP2 B DC 16 ? ? 105.35 119.60 -14.25 1.50 N 57 1 "O4'" B DC 16 ? ? "C1'" B DC 16 ? ? N1 B DC 16 ? ? 111.28 108.30 2.98 0.30 N 58 1 N1 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 123.16 118.90 4.26 0.60 N 59 1 N3 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 115.86 121.90 -6.04 0.70 N 60 1 OP1 B DT 17 ? ? P B DT 17 ? ? OP2 B DT 17 ? ? 105.35 119.60 -14.25 1.50 N 61 1 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 110.91 108.30 2.61 0.30 N 62 1 N3 B DT 17 ? ? C2 B DT 17 ? ? O2 B DT 17 ? ? 118.63 122.30 -3.67 0.60 N 63 1 OP1 B DA 18 ? ? P B DA 18 ? ? OP2 B DA 18 ? ? 105.07 119.60 -14.53 1.50 N 64 1 N1 B DA 18 ? ? C2 B DA 18 ? ? N3 B DA 18 ? ? 123.83 129.30 -5.47 0.50 N 65 1 C2 B DA 18 ? ? N3 B DA 18 ? ? C4 B DA 18 ? ? 113.66 110.60 3.06 0.50 N 66 1 N9 B DA 18 ? ? C4 B DA 18 ? ? C5 B DA 18 ? ? 108.21 105.80 2.41 0.40 N 67 1 OP1 B DG 19 ? ? P B DG 19 ? ? OP2 B DG 19 ? ? 105.51 119.60 -14.09 1.50 N 68 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 110.75 108.30 2.45 0.30 N 69 1 N3 B DG 19 ? ? C4 B DG 19 ? ? C5 B DG 19 ? ? 125.50 128.60 -3.10 0.50 N 70 1 N9 B DG 19 ? ? C4 B DG 19 ? ? C5 B DG 19 ? ? 108.82 105.40 3.42 0.40 N 71 1 OP1 B DC 20 ? ? P B DC 20 ? ? OP2 B DC 20 ? ? 105.34 119.60 -14.26 1.50 N 72 1 N1 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 122.81 118.90 3.91 0.60 N 73 1 N3 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 116.04 121.90 -5.86 0.70 N 74 1 OP1 B DT 21 ? ? P B DT 21 ? ? OP2 B DT 21 ? ? 105.31 119.60 -14.29 1.50 N 75 1 "O4'" B DT 21 ? ? "C1'" B DT 21 ? ? N1 B DT 21 ? ? 111.52 108.30 3.22 0.30 N 76 1 N3 B DT 21 ? ? C2 B DT 21 ? ? O2 B DT 21 ? ? 118.56 122.30 -3.74 0.60 N 77 1 OP1 B DA 22 ? ? P B DA 22 ? ? OP2 B DA 22 ? ? 105.04 119.60 -14.56 1.50 N 78 1 "O4'" B DA 22 ? ? "C1'" B DA 22 ? ? N9 B DA 22 ? ? 110.54 108.30 2.24 0.30 N 79 1 N1 B DA 22 ? ? C2 B DA 22 ? ? N3 B DA 22 ? ? 124.32 129.30 -4.98 0.50 N 80 1 C2 B DA 22 ? ? N3 B DA 22 ? ? C4 B DA 22 ? ? 114.40 110.60 3.80 0.50 N 81 1 C5 B DA 22 ? ? C6 B DA 22 ? ? N1 B DA 22 ? ? 122.59 117.70 4.89 0.50 N 82 1 C5 B DA 22 ? ? N7 B DA 22 ? ? C8 B DA 22 ? ? 100.56 103.90 -3.34 0.50 N 83 1 OP1 B DG 23 ? ? P B DG 23 ? ? OP2 B DG 23 ? ? 105.08 119.60 -14.52 1.50 N 84 1 N3 B DG 23 ? ? C4 B DG 23 ? ? C5 B DG 23 ? ? 125.32 128.60 -3.28 0.50 N 85 1 N9 B DG 23 ? ? C4 B DG 23 ? ? C5 B DG 23 ? ? 108.83 105.40 3.43 0.40 N 86 1 OP1 B DC 24 ? ? P B DC 24 ? ? OP2 B DC 24 ? ? 105.27 119.60 -14.33 1.50 N 87 1 "O4'" B DC 24 ? ? "C1'" B DC 24 ? ? N1 B DC 24 ? ? 111.60 108.30 3.30 0.30 N 88 1 N1 B DC 24 ? ? C2 B DC 24 ? ? O2 B DC 24 ? ? 122.73 118.90 3.83 0.60 N 89 1 N3 B DC 24 ? ? C2 B DC 24 ? ? O2 B DC 24 ? ? 116.17 121.90 -5.73 0.70 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 7 ? ? 0.069 'SIDE CHAIN' 2 1 DC A 12 ? ? 0.063 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2KAR 'double helix' 2KAR 'b-form double helix' 2KAR '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 12 1_555 -0.492 -0.079 0.093 -0.628 -5.021 -1.310 1 A_DG1:DC24_B A 1 ? B 24 ? 19 1 1 A DC 2 1_555 B DG 11 1_555 0.327 -0.066 0.284 -3.732 -6.188 -2.106 2 A_DC2:DG23_B A 2 ? B 23 ? 19 1 1 A DT 3 1_555 B DA 10 1_555 0.036 -0.010 0.086 3.317 -8.478 -3.900 3 A_DT3:DA22_B A 3 ? B 22 ? 20 1 1 A DA 4 1_555 B DT 9 1_555 -0.022 0.014 -0.010 1.208 -11.083 -6.066 4 A_DA4:DT21_B A 4 ? B 21 ? 20 1 1 A DG 5 1_555 B DC 8 1_555 -0.441 -0.095 0.188 0.283 0.590 -1.693 5 A_DG5:DC20_B A 5 ? B 20 ? 19 1 1 A DC 6 1_555 B DG 7 1_555 0.482 -0.063 -0.081 14.648 -1.584 -0.260 6 A_DC6:DG19_B A 6 ? B 19 ? 19 1 1 A DG 7 1_555 B DA 6 1_555 -0.123 -4.705 -0.076 32.021 -23.970 80.726 7 A_DG7:DA18_B A 7 ? B 18 ? ? ? 1 A DA 8 1_555 B DT 5 1_555 0.085 0.024 0.145 31.679 -29.389 -3.150 8 A_DA8:DT17_B A 8 ? B 17 ? 20 1 1 A DG 9 1_555 B DC 4 1_555 -0.519 -0.139 0.308 2.922 -17.044 -2.075 9 A_DG9:DC16_B A 9 ? B 16 ? 19 1 1 A DT 10 1_555 B DA 3 1_555 -0.038 0.032 -0.090 -1.497 -14.684 -6.371 10 A_DT10:DA15_B A 10 ? B 15 ? 20 1 1 A DC 11 1_555 B DG 2 1_555 0.477 -0.113 -0.029 -9.542 -11.192 -0.828 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DC 12 1_555 B DG 1 1_555 0.501 -0.087 0.028 -4.065 0.267 -1.798 12 A_DC12:DG13_B A 12 ? B 13 ? 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 12 1_555 A DC 2 1_555 B DG 11 1_555 -0.389 -0.571 3.449 -2.174 -1.398 33.735 -0.741 0.295 3.487 -2.404 3.739 33.831 1 AA_DG1DC2:DG23DC24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DC 2 1_555 B DG 11 1_555 A DT 3 1_555 B DA 10 1_555 0.141 -0.829 3.120 1.246 -0.042 34.060 -1.407 -0.052 3.124 -0.071 -2.127 34.082 2 AA_DC2DT3:DA22DG23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DT 3 1_555 B DA 10 1_555 A DA 4 1_555 B DT 9 1_555 0.043 -1.386 3.236 -0.003 10.285 31.595 -4.025 -0.075 2.667 18.292 0.005 33.186 3 AA_DT3DA4:DT21DA22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DA 4 1_555 B DT 9 1_555 A DG 5 1_555 B DC 8 1_555 0.022 -1.273 3.262 -2.063 0.931 31.421 -2.517 -0.422 3.216 1.717 3.804 31.500 4 AA_DA4DG5:DC20DT21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DG 5 1_555 B DC 8 1_555 A DC 6 1_555 B DG 7 1_555 0.303 0.064 3.058 3.287 2.589 36.966 -0.224 -0.065 3.070 4.067 -5.163 37.194 5 AA_DG5DC6:DG19DC20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DC 6 1_555 B DG 7 1_555 A DG 7 1_555 B DA 6 1_555 1.635 -3.822 1.843 -164.812 18.518 96.051 -1.957 -1.172 0.008 9.460 84.198 170.549 6 AA_DC6DG7:DA18DG19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DG 7 1_555 B DA 6 1_555 A DA 8 1_555 B DT 5 1_555 -3.254 -1.083 -2.018 126.839 -113.310 96.080 -1.137 0.964 -2.641 -57.499 -64.365 173.372 7 AA_DG7DA8:DT17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DA 8 1_555 B DT 5 1_555 A DG 9 1_555 B DC 4 1_555 0.081 -0.996 3.893 -4.895 11.168 34.239 -3.390 -0.914 3.372 18.266 8.006 36.284 8 AA_DA8DG9:DC16DT17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DG 9 1_555 B DC 4 1_555 A DT 10 1_555 B DA 3 1_555 -0.348 -0.620 3.333 3.469 1.258 34.262 -1.244 1.133 3.259 2.127 -5.867 34.454 9 AA_DG9DT10:DA15DC16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DT 10 1_555 B DA 3 1_555 A DC 11 1_555 B DG 2 1_555 0.285 -0.168 3.357 0.194 1.629 41.546 -0.414 -0.380 3.349 2.295 -0.273 41.577 10 AA_DT10DC11:DG14DA15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DC 12 1_555 B DG 1 1_555 1.308 -0.162 3.248 -0.863 -0.156 31.927 -0.267 -2.532 3.214 -0.283 1.569 31.938 11 AA_DC11DC12:DG13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name '(4S)-nonane-1,4-diol' _pdbx_entity_nonpoly.comp_id HND #