data_193D # _entry.id 193D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 193D WWPDB D_1000170207 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 185D unspecified 'SOLUTION STRUCTURE OF D(GACGTC) COMPLEXED WITH TRIOSTIN A' PDB 1PFE unspecified 'CRYSTAL STRUCTURE OF D(GCGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P6322' PDB 1VS2 unspecified 'CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A' PDB 1XVK unspecified 'CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632' PDB 1XVN unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632' PDB 1XVR unspecified 'CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP C21' PDB 2ADW unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P42212' PDB 2DA8 unspecified 'SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN A AT POSITIONS 4 AND 8' PDB 3GO3 unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P41212' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 193D _pdbx_database_status.recvd_initial_deposition_date 1994-09-30 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Chen, H.' 1 'Patel, D.J.' 2 # _citation.id primary _citation.title 'Solution Structure of a Quinomycin Bisintercalator-DNA Complex.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 246 _citation.page_first 164 _citation.page_last ? _citation.year 1995 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 7853395 _citation.pdbx_database_id_DOI 10.1006/JMBI.1994.0074 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Chen, H.' 1 primary 'Patel, D.J.' 2 # _cell.entry_id 193D _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 193D _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(*AP*CP*AP*CP*GP*TP*GP*T)-3') ; 2426.617 2 ? ? ? ? 2 polymer syn QUINOMYCIN 847.056 1 ? ? ? ? 3 non-polymer syn '3-HYDROXYQUINALDIC ACID' 189.167 2 ? ? ? ? # _entity_name_com.entity_id 2 _entity_name_com.name 'QUINOMYCIN A, UK-63052' # 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 '(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DT)' ACACGTGT A,B ? 2 'polypeptide(L)' no yes '(DSN)A(NYB)(CPC)(DSN)A(NCY)(CPC)' SAXXSAXX C ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DC n 1 3 DA n 1 4 DC n 1 5 DG n 1 6 DT n 1 7 DG n 1 8 DT n 2 1 DSN n 2 2 ALA n 2 3 NYB n 2 4 CPC n 2 5 DSN n 2 6 ALA n 2 7 NCY n 2 8 CPC 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 ? ? STREPTOMYCES ? ? 'CHEMICALLY SYNTHESIZED' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 193D 1 ? ? 193D ? 2 PDB 193D 2 ? ? 193D ? # 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 193D A 1 ? 8 ? 193D 1 ? 8 ? 1 8 2 1 193D B 1 ? 8 ? 193D 1 ? 8 ? 1 8 3 2 193D C 1 ? 8 ? 193D 1 ? 8 ? 1 8 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 CPC 'L-peptide linking' . '2-METHYL-1-METHYLAMINO-CYCLOPROPANE CARBOXYLIC ACID' ? 'C6 H11 N O2' 129.157 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 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HQU non-polymer . '3-HYDROXYQUINALDIC ACID' ? 'C10 H7 N O3' 189.167 NCY 'L-peptide linking' . N-METHYLCYSTEINE ? 'C4 H9 N O2 S' 135.185 NYB 'L-peptide linking' n 'N-METHYL-S-[(1R)-1-METHYLPROPYL]-L-CYSTEINE' ? 'C8 H17 N O2 S' 191.291 # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents ? _pdbx_nmr_sample_details.solvent_system D2O # _pdbx_nmr_refine.entry_id 193D _pdbx_nmr_refine.method 'MOLECULAR DYNAMICS, MATRIX RELAXATION' _pdbx_nmr_refine.details ;TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE- RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. TWO INITIAL VELOCITY SEEDS WERE USED FOR EACH STARTING STRUCTURE WHICH YIELDS FOUR DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 0.5 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 120 AND 180 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 R(1/6) FACTOR 0.023 0.024 0.024 0.026 BOND (ANG) 0.011 0.011 0.011 0.011 ANGLES (DEG) 3.616 3.657 3.700 3.725 IMPROPERS (DEG) 0.274 0.285 0.241 0.298 ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 193D _pdbx_nmr_ensemble.conformers_calculated_total_number 4 _pdbx_nmr_ensemble.conformers_submitted_total_number 4 _pdbx_nmr_ensemble.conformer_selection_criteria 'all calculated structures submitted' _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.classification refinement _pdbx_nmr_software.name X-PLOR _pdbx_nmr_software.version ? _pdbx_nmr_software.authors BRUNGER _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 193D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 193D _struct.title 'SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX' _struct.pdbx_descriptor 'QUINOMYCIN/DNA Complex, 3-HYDROXYQUINALDIC ACID' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 193D _struct_keywords.pdbx_keywords DNA/ANTIBIOTIC _struct_keywords.text 'BISINTERCALATOR, DEPSIPEPTIDE, QUINOXALINE, THIOACETAL, ANTIBIOTIC, ANTITUMOR, DNA-ANTIBIOTIC COMPLEX' # 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # 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 covale1 covale ? ? D HQU . C ? ? ? 1_555 C DSN 1 N ? ? C HQU 0 C DSN 1 1_555 ? ? ? ? ? ? ? 1.312 ? covale2 covale ? ? C DSN 1 C ? ? ? 1_555 C ALA 2 N ? ? C DSN 1 C ALA 2 1_555 ? ? ? ? ? ? ? 1.314 ? covale3 covale ? ? C DSN 1 OG ? ? ? 1_555 C CPC 8 C ? ? C DSN 1 C CPC 8 1_555 ? ? ? ? ? ? ? 1.386 ? covale4 covale ? ? C ALA 2 C ? ? ? 1_555 C NYB 3 N ? ? C ALA 2 C NYB 3 1_555 ? ? ? ? ? ? ? 1.333 ? covale5 covale ? ? C NYB 3 CB ? ? ? 1_555 C NCY 7 SG ? ? C NYB 3 C NCY 7 1_555 ? ? ? ? ? ? ? 1.808 ? covale6 covale ? ? C NYB 3 C ? ? ? 1_555 C CPC 4 N ? ? C NYB 3 C CPC 4 1_555 ? ? ? ? ? ? ? 1.332 ? covale7 covale ? ? C CPC 4 C ? ? ? 1_555 C DSN 5 OG ? ? C CPC 4 C DSN 5 1_555 ? ? ? ? ? ? ? 1.394 ? covale8 covale ? ? C DSN 5 C ? ? ? 1_555 C ALA 6 N ? ? C DSN 5 C ALA 6 1_555 ? ? ? ? ? ? ? 1.312 ? covale9 covale ? ? C DSN 5 N ? ? ? 1_555 E HQU . C ? ? C DSN 5 C HQU 9 1_555 ? ? ? ? ? ? ? 1.313 ? covale10 covale ? ? C ALA 6 C ? ? ? 1_555 C NCY 7 N ? ? C ALA 6 C NCY 7 1_555 ? ? ? ? ? ? ? 1.332 ? covale11 covale ? ? C NCY 7 C ? ? ? 1_555 C CPC 8 N ? ? C NCY 7 C CPC 8 1_555 ? ? ? ? ? ? ? 1.326 ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 1 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 1 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 2 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 2 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 2 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 3 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 3 B DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 4 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 4 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 4 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 5 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 5 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 5 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 6 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 6 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 7 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 7 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 7 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 8 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 8 B DA 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 ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 8 _struct_site.details 'BINDING SITE FOR CHAIN C OF QUINOMYCIN' # 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 8 DA A 3 ? DA A 3 . ? 1_555 ? 2 AC1 8 DC A 4 ? DC A 4 . ? 1_555 ? 3 AC1 8 DG A 5 ? DG A 5 . ? 1_555 ? 4 AC1 8 DT A 6 ? DT A 6 . ? 1_555 ? 5 AC1 8 DA B 3 ? DA B 3 . ? 1_555 ? 6 AC1 8 DC B 4 ? DC B 4 . ? 1_555 ? 7 AC1 8 DG B 5 ? DG B 5 . ? 1_555 ? 8 AC1 8 DT B 6 ? DT B 6 . ? 1_555 ? # _database_PDB_matrix.entry_id 193D _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 193D _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_sites_footnote.id _atom_sites_footnote.text 1 'ALA D 2 - CYS D 3 MODEL 1 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION' 2 'ALA C 2 - CYS C 3 MODEL 2 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION' 3 'ALA D 2 - CYS D 3 MODEL 3 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION' 4 'ALA D 2 - CYS D 3 MODEL 4 OMEGA = 359.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION' 7 'SER C 1 IS A D-SERINE.' 8 'SER D 1 IS A D-SERINE.' # loop_ _atom_type.symbol C H N O P S # 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 DA 1 1 1 DA DA A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DT 8 8 8 DT DT A . n B 1 1 DA 1 1 1 DA DA B . n B 1 2 DC 2 2 2 DC DC B . n B 1 3 DA 3 3 3 DA DA B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DG 5 5 5 DG DG B . n B 1 6 DT 6 6 6 DT DT B . n B 1 7 DG 7 7 7 DG DG B . n B 1 8 DT 8 8 8 DT DT B . n C 2 1 DSN 1 1 1 DSN DSN C . n C 2 2 ALA 2 2 2 ALA ALA C . n C 2 3 NYB 3 3 3 NYB NYB C . n C 2 4 CPC 4 4 4 CPC CPC C . n C 2 5 DSN 5 5 5 DSN DSN C . n C 2 6 ALA 6 6 6 ALA ALA C . n C 2 7 NCY 7 7 7 NCY NCY C . n C 2 8 CPC 8 8 8 CPC CPC C . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 3 HQU 1 0 0 HQU HQU C . E 3 HQU 1 9 9 HQU HQU C . # _pdbx_molecule_features.prd_id PRD_000492 _pdbx_molecule_features.name uk63052 _pdbx_molecule_features.type 'Cyclic depsipeptide' _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;QUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO HYDROXYQUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000492 C 1 PRD_000492 D 1 PRD_000492 E # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _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 1995-02-27 2 'Structure model' 1 1 2011-06-14 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-07-27 5 'Structure model' 1 4 2012-12-12 6 'Structure model' 2 0 2017-11-01 # _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 ? # 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' 'Atomic model' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Non-polymer description' 7 4 'Structure model' 'Structure summary' 8 5 'Structure model' Other 9 6 'Structure model' Advisory 10 6 'Structure model' 'Atomic model' 11 6 'Structure model' 'Derived calculations' 12 6 '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 6 'Structure model' atom_site 2 6 'Structure model' pdbx_database_status 3 6 'Structure model' pdbx_struct_assembly 4 6 'Structure model' pdbx_struct_oper_list 5 6 'Structure model' pdbx_validate_polymer_linkage # 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 6 'Structure model' '_atom_site.auth_atom_id' 2 6 'Structure model' '_atom_site.label_atom_id' 3 6 'Structure model' '_pdbx_database_status.process_site' 4 6 'Structure model' '_pdbx_struct_assembly.details' 5 6 'Structure model' '_pdbx_struct_assembly.method_details' 6 6 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 X-PLOR refinement . ? 2 X-PLOR phasing . ? 3 # _pdbx_entry_details.entry_id 193D _pdbx_entry_details.compound_details ;QUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, QUINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) HQU ; _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 C8 A DA 1 ? ? N9 A DA 1 ? ? 1.325 1.373 -0.048 0.008 N 2 1 C5 A DT 8 ? ? C7 A DT 8 ? ? 1.536 1.496 0.040 0.006 N 3 1 C5 B DT 6 ? ? C7 B DT 6 ? ? 1.537 1.496 0.041 0.006 N 4 1 C5 B DT 8 ? ? C7 B DT 8 ? ? 1.535 1.496 0.039 0.006 N 5 2 C8 A DA 1 ? ? N9 A DA 1 ? ? 1.324 1.373 -0.049 0.008 N 6 2 C8 B DA 1 ? ? N9 B DA 1 ? ? 1.325 1.373 -0.048 0.008 N 7 2 C5 B DT 6 ? ? C7 B DT 6 ? ? 1.533 1.496 0.037 0.006 N 8 2 C5 B DT 8 ? ? C7 B DT 8 ? ? 1.534 1.496 0.038 0.006 N 9 3 C8 A DA 1 ? ? N9 A DA 1 ? ? 1.323 1.373 -0.050 0.008 N 10 3 C5 A DT 8 ? ? C7 A DT 8 ? ? 1.536 1.496 0.040 0.006 N 11 3 C8 B DA 1 ? ? N9 B DA 1 ? ? 1.324 1.373 -0.049 0.008 N 12 3 C5 B DT 8 ? ? C7 B DT 8 ? ? 1.537 1.496 0.041 0.006 N 13 4 C8 A DA 1 ? ? N9 A DA 1 ? ? 1.320 1.373 -0.053 0.008 N 14 4 C8 B DA 1 ? ? N9 B DA 1 ? ? 1.322 1.373 -0.051 0.008 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N7 A DA 1 ? ? C8 A DA 1 ? ? N9 A DA 1 ? ? 118.09 113.80 4.29 0.50 N 2 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 103.76 108.00 -4.24 0.70 N 3 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? "C2'" A DG 5 ? ? 100.47 105.90 -5.43 0.80 N 4 1 N7 A DG 5 ? ? C8 A DG 5 ? ? N9 A DG 5 ? ? 116.27 113.10 3.17 0.50 N 5 1 C8 A DG 5 ? ? N9 A DG 5 ? ? C4 A DG 5 ? ? 103.87 106.40 -2.53 0.40 N 6 1 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 110.76 108.30 2.46 0.30 N 7 1 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 118.46 122.90 -4.44 0.60 N 8 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 111.03 108.30 2.72 0.30 N 9 1 N7 A DG 7 ? ? C8 A DG 7 ? ? N9 A DG 7 ? ? 116.19 113.10 3.09 0.50 N 10 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 110.55 108.30 2.25 0.30 N 11 1 N7 B DA 1 ? ? C8 B DA 1 ? ? N9 B DA 1 ? ? 117.96 113.80 4.16 0.50 N 12 1 N1 B DC 2 ? ? C2 B DC 2 ? ? O2 B DC 2 ? ? 122.53 118.90 3.63 0.60 N 13 1 "C3'" B DC 2 ? ? "O3'" B DC 2 ? ? P B DA 3 ? ? 127.28 119.70 7.58 1.20 Y 14 1 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 110.78 108.30 2.48 0.30 N 15 1 N1 B DC 4 ? ? C2 B DC 4 ? ? O2 B DC 4 ? ? 123.04 118.90 4.14 0.60 N 16 1 "C1'" B DT 6 ? ? "O4'" B DT 6 ? ? "C4'" B DT 6 ? ? 103.55 110.10 -6.55 1.00 N 17 1 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 113.27 108.30 4.97 0.30 N 18 1 "O4'" B DG 7 ? ? "C1'" B DG 7 ? ? N9 B DG 7 ? ? 111.02 108.30 2.72 0.30 N 19 1 N7 B DG 7 ? ? C8 B DG 7 ? ? N9 B DG 7 ? ? 116.12 113.10 3.02 0.50 N 20 1 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? N1 B DT 8 ? ? 110.71 108.30 2.41 0.30 N 21 2 N7 A DA 1 ? ? C8 A DA 1 ? ? N9 A DA 1 ? ? 118.01 113.80 4.21 0.50 N 22 2 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 103.79 108.00 -4.21 0.70 N 23 2 "C3'" A DC 2 ? ? "O3'" A DC 2 ? ? P A DA 3 ? ? 128.26 119.70 8.56 1.20 Y 24 2 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 111.79 108.30 3.49 0.30 N 25 2 N1 A DC 4 ? ? C2 A DC 4 ? ? O2 A DC 4 ? ? 122.96 118.90 4.06 0.60 N 26 2 N7 A DG 5 ? ? C8 A DG 5 ? ? N9 A DG 5 ? ? 116.61 113.10 3.51 0.50 N 27 2 C8 A DG 5 ? ? N9 A DG 5 ? ? C4 A DG 5 ? ? 103.67 106.40 -2.73 0.40 N 28 2 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.23 108.30 1.93 0.30 N 29 2 N7 A DG 7 ? ? C8 A DG 7 ? ? N9 A DG 7 ? ? 116.38 113.10 3.28 0.50 N 30 2 C8 A DG 7 ? ? N9 A DG 7 ? ? C4 A DG 7 ? ? 103.97 106.40 -2.43 0.40 N 31 2 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 111.46 108.30 3.16 0.30 N 32 2 C5 B DA 1 ? ? N7 B DA 1 ? ? C8 B DA 1 ? ? 100.85 103.90 -3.05 0.50 N 33 2 N7 B DA 1 ? ? C8 B DA 1 ? ? N9 B DA 1 ? ? 118.19 113.80 4.39 0.50 N 34 2 "C5'" B DC 2 ? ? "C4'" B DC 2 ? ? "C3'" B DC 2 ? ? 122.94 115.70 7.24 1.20 N 35 2 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 103.71 108.00 -4.29 0.70 N 36 2 "C3'" B DC 2 ? ? "O3'" B DC 2 ? ? P B DA 3 ? ? 129.46 119.70 9.76 1.20 Y 37 2 "O4'" B DA 3 ? ? "C1'" B DA 3 ? ? N9 B DA 3 ? ? 112.95 108.30 4.65 0.30 N 38 2 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 113.69 108.30 5.39 0.30 N 39 2 N1 B DC 4 ? ? C2 B DC 4 ? ? O2 B DC 4 ? ? 122.83 118.90 3.93 0.60 N 40 2 "O4'" B DG 5 ? ? "C1'" B DG 5 ? ? N9 B DG 5 ? ? 111.93 108.30 3.63 0.30 N 41 2 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 110.92 108.30 2.62 0.30 N 42 2 "O4'" B DG 7 ? ? "C1'" B DG 7 ? ? N9 B DG 7 ? ? 110.27 108.30 1.97 0.30 N 43 2 N7 B DG 7 ? ? C8 B DG 7 ? ? N9 B DG 7 ? ? 116.34 113.10 3.24 0.50 N 44 2 C8 B DG 7 ? ? N9 B DG 7 ? ? C4 B DG 7 ? ? 103.99 106.40 -2.41 0.40 N 45 2 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? N1 B DT 8 ? ? 111.65 108.30 3.35 0.30 N 46 3 "O4'" A DA 1 ? ? "C1'" A DA 1 ? ? N9 A DA 1 ? ? 112.47 108.30 4.17 0.30 N 47 3 C5 A DA 1 ? ? N7 A DA 1 ? ? C8 A DA 1 ? ? 100.82 103.90 -3.08 0.50 N 48 3 N7 A DA 1 ? ? C8 A DA 1 ? ? N9 A DA 1 ? ? 118.40 113.80 4.60 0.50 N 49 3 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 103.34 108.00 -4.66 0.70 N 50 3 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 123.10 118.90 4.20 0.60 N 51 3 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? "C2'" A DA 3 ? ? 100.87 105.90 -5.03 0.80 N 52 3 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 110.88 108.30 2.58 0.30 N 53 3 N1 A DC 4 ? ? C2 A DC 4 ? ? O2 A DC 4 ? ? 122.76 118.90 3.86 0.60 N 54 3 "C3'" A DC 4 ? ? "O3'" A DC 4 ? ? P A DG 5 ? ? 129.71 119.70 10.01 1.20 Y 55 3 N7 A DG 5 ? ? C8 A DG 5 ? ? N9 A DG 5 ? ? 116.46 113.10 3.36 0.50 N 56 3 C8 A DG 5 ? ? N9 A DG 5 ? ? C4 A DG 5 ? ? 103.72 106.40 -2.68 0.40 N 57 3 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 119.06 122.90 -3.84 0.60 N 58 3 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 111.02 108.30 2.72 0.30 N 59 3 N7 A DG 7 ? ? C8 A DG 7 ? ? N9 A DG 7 ? ? 116.59 113.10 3.49 0.50 N 60 3 C8 A DG 7 ? ? N9 A DG 7 ? ? C4 A DG 7 ? ? 103.99 106.40 -2.41 0.40 N 61 3 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 110.72 108.30 2.42 0.30 N 62 3 "O4'" B DA 1 ? ? "C1'" B DA 1 ? ? N9 B DA 1 ? ? 112.57 108.30 4.27 0.30 N 63 3 C5 B DA 1 ? ? N7 B DA 1 ? ? C8 B DA 1 ? ? 100.84 103.90 -3.06 0.50 N 64 3 N7 B DA 1 ? ? C8 B DA 1 ? ? N9 B DA 1 ? ? 118.43 113.80 4.63 0.50 N 65 3 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 103.23 108.00 -4.77 0.70 N 66 3 N1 B DC 2 ? ? C2 B DC 2 ? ? O2 B DC 2 ? ? 123.08 118.90 4.18 0.60 N 67 3 N1 B DC 4 ? ? C2 B DC 4 ? ? O2 B DC 4 ? ? 122.93 118.90 4.03 0.60 N 68 3 N7 B DG 5 ? ? C8 B DG 5 ? ? N9 B DG 5 ? ? 116.26 113.10 3.16 0.50 N 69 3 C8 B DG 5 ? ? N9 B DG 5 ? ? C4 B DG 5 ? ? 103.67 106.40 -2.73 0.40 N 70 3 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 112.28 108.30 3.98 0.30 N 71 3 C6 B DT 6 ? ? C5 B DT 6 ? ? C7 B DT 6 ? ? 118.92 122.90 -3.98 0.60 N 72 3 "O4'" B DG 7 ? ? "C1'" B DG 7 ? ? N9 B DG 7 ? ? 111.05 108.30 2.75 0.30 N 73 3 N7 B DG 7 ? ? C8 B DG 7 ? ? N9 B DG 7 ? ? 116.64 113.10 3.54 0.50 N 74 3 C8 B DG 7 ? ? N9 B DG 7 ? ? C4 B DG 7 ? ? 103.95 106.40 -2.45 0.40 N 75 3 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? N1 B DT 8 ? ? 110.52 108.30 2.22 0.30 N 76 4 "O4'" A DA 1 ? ? "C1'" A DA 1 ? ? N9 A DA 1 ? ? 110.61 108.30 2.31 0.30 N 77 4 C5 A DA 1 ? ? N7 A DA 1 ? ? C8 A DA 1 ? ? 100.80 103.90 -3.10 0.50 N 78 4 N7 A DA 1 ? ? C8 A DA 1 ? ? N9 A DA 1 ? ? 118.24 113.80 4.44 0.50 N 79 4 "C5'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 122.95 115.70 7.25 1.20 N 80 4 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 100.63 108.00 -7.37 0.70 N 81 4 "C3'" A DC 2 ? ? "O3'" A DC 2 ? ? P A DA 3 ? ? 128.25 119.70 8.55 1.20 Y 82 4 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 112.36 108.30 4.06 0.30 N 83 4 N1 A DC 4 ? ? C2 A DC 4 ? ? O2 A DC 4 ? ? 122.71 118.90 3.81 0.60 N 84 4 N7 A DG 5 ? ? C8 A DG 5 ? ? N9 A DG 5 ? ? 116.48 113.10 3.38 0.50 N 85 4 C8 A DG 5 ? ? N9 A DG 5 ? ? C4 A DG 5 ? ? 103.63 106.40 -2.77 0.40 N 86 4 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? "C2'" A DT 6 ? ? 100.55 105.90 -5.35 0.80 N 87 4 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 115.58 108.30 7.28 0.30 N 88 4 "C5'" A DT 8 ? ? "C4'" A DT 8 ? ? "O4'" A DT 8 ? ? 119.69 109.80 9.89 1.10 N 89 4 "O4'" B DA 1 ? ? "C1'" B DA 1 ? ? N9 B DA 1 ? ? 110.78 108.30 2.48 0.30 N 90 4 N7 B DA 1 ? ? C8 B DA 1 ? ? N9 B DA 1 ? ? 118.07 113.80 4.27 0.50 N 91 4 "O4'" B DC 2 ? ? "C4'" B DC 2 ? ? "C3'" B DC 2 ? ? 109.79 106.00 3.79 0.60 N 92 4 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 100.48 108.00 -7.52 0.70 N 93 4 "O4'" B DA 3 ? ? "C1'" B DA 3 ? ? N9 B DA 3 ? ? 115.32 108.30 7.02 0.30 N 94 4 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 112.85 108.30 4.55 0.30 N 95 4 "O4'" B DG 5 ? ? "C1'" B DG 5 ? ? N9 B DG 5 ? ? 110.20 108.30 1.90 0.30 N 96 4 N7 B DG 5 ? ? C8 B DG 5 ? ? N9 B DG 5 ? ? 116.40 113.10 3.30 0.50 N 97 4 C8 B DG 5 ? ? N9 B DG 5 ? ? C4 B DG 5 ? ? 103.93 106.40 -2.47 0.40 N 98 4 "O4'" B DT 6 ? ? "C1'" B DT 6 ? ? N1 B DT 6 ? ? 111.53 108.30 3.23 0.30 N 99 4 C6 B DT 6 ? ? C5 B DT 6 ? ? C7 B DT 6 ? ? 118.52 122.90 -4.38 0.60 N 100 4 "O4'" B DG 7 ? ? "C1'" B DG 7 ? ? N9 B DG 7 ? ? 115.44 108.30 7.14 0.30 N 101 4 "C5'" B DT 8 ? ? "C4'" B DT 8 ? ? "O4'" B DT 8 ? ? 119.27 109.80 9.47 1.10 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 193D 'double helix' 193D '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 DA 1 1_555 B DT 8 1_555 -0.006 -0.210 -0.134 -20.633 -17.637 -1.999 1 A_DA1:DT8_B A 1 ? B 8 ? 20 1 1 A DC 2 1_555 B DG 7 1_555 0.561 -0.284 0.357 -17.459 -0.855 -1.260 2 A_DC2:DG7_B A 2 ? B 7 ? 19 1 1 A DA 3 1_555 B DT 6 1_555 0.436 -0.145 0.197 9.576 -1.872 -2.211 3 A_DA3:DT6_B A 3 ? B 6 ? 20 1 1 A DC 4 1_555 B DG 5 1_555 0.957 -0.358 0.495 -21.667 5.574 0.200 4 A_DC4:DG5_B A 4 ? B 5 ? 19 1 1 A DG 5 1_555 B DC 4 1_555 -0.632 -0.317 0.355 20.252 1.744 -4.361 5 A_DG5:DC4_B A 5 ? B 4 ? 19 1 1 A DT 6 1_555 B DA 3 1_555 -0.348 -0.221 0.256 -6.019 -0.421 0.338 6 A_DT6:DA3_B A 6 ? B 3 ? 20 1 1 A DG 7 1_555 B DC 2 1_555 -0.474 -0.281 0.181 16.481 1.863 -1.791 7 A_DG7:DC2_B A 7 ? B 2 ? 19 1 1 A DT 8 1_555 B DA 1 1_555 -0.025 -0.167 -0.331 26.186 -14.958 -1.220 8 A_DT8:DA1_B A 8 ? B 1 ? 20 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 DA 1 1_555 B DT 8 1_555 A DC 2 1_555 B DG 7 1_555 -0.570 -0.857 3.271 -1.514 3.381 29.951 -2.327 0.791 3.182 6.511 2.915 30.174 1 AA_DA1DC2:DG7DT8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A DC 2 1_555 B DG 7 1_555 A DA 3 1_555 B DT 6 1_555 -0.102 -1.133 2.364 1.121 10.435 22.172 -4.761 0.466 1.661 25.384 -2.727 24.502 2 AA_DC2DA3:DT6DG7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A DA 3 1_555 B DT 6 1_555 A DC 4 1_555 B DG 5 1_555 0.664 1.223 7.172 4.711 4.317 21.964 -0.377 2.102 7.256 11.035 -12.041 22.863 3 AA_DA3DC4:DG5DT6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A DC 4 1_555 B DG 5 1_555 A DG 5 1_555 B DC 4 1_555 -0.191 2.795 2.438 0.392 -2.839 1.607 60.805 4.988 -1.245 -60.162 -8.303 3.286 4 AA_DC4DG5:DC4DG5_BB A 4 ? B 5 ? A 5 ? B 4 ? 1 A DG 5 1_555 B DC 4 1_555 A DT 6 1_555 B DA 3 1_555 -0.847 1.216 6.967 -9.428 2.267 21.042 1.291 -5.124 6.800 5.826 24.227 23.146 5 AA_DG5DT6:DA3DC4_BB A 5 ? B 4 ? A 6 ? B 3 ? 1 A DT 6 1_555 B DA 3 1_555 A DG 7 1_555 B DC 2 1_555 -0.161 -1.231 2.456 0.441 7.177 22.017 -4.794 0.508 1.957 18.180 -1.116 23.147 6 AA_DT6DG7:DC2DA3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A DG 7 1_555 B DC 2 1_555 A DT 8 1_555 B DA 1 1_555 0.756 -0.929 3.014 1.385 0.716 29.073 -1.993 -1.224 3.022 1.424 -2.757 29.114 7 AA_DG7DT8:DA1DC2_BB A 7 ? B 2 ? A 8 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name '3-HYDROXYQUINALDIC ACID' _pdbx_entity_nonpoly.comp_id HQU #