data_1AL9 # _entry.id 1AL9 # _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 1AL9 pdb_00001al9 10.2210/pdb1al9/pdb WWPDB D_1000170956 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1AMD _pdbx_database_related.details 'MINIMIZED AVERAGE STRUCTURE' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1AL9 _pdbx_database_status.recvd_initial_deposition_date 1997-06-12 _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 'Robinson, H.' 1 'Wang, A.H.-J.' 2 # _citation.id primary _citation.title 'Binding of two novel bisdaunorubicins to DNA studied by NMR spectroscopy.' _citation.journal_abbrev Biochemistry _citation.journal_volume 36 _citation.page_first 8663 _citation.page_last 8670 _citation.year 1997 _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 9289011 _citation.pdbx_database_id_DOI 10.1021/bi970842j # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Robinson, H.' 1 ? primary 'Priebe, W.' 2 ? primary 'Chaires, J.B.' 3 ? primary 'Wang, A.H.' 4 ? # _cell.entry_id 1AL9 _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 1AL9 _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*GP*TP*AP*CP*GP*T)-3') ; 2426.617 2 ? ? ? 'WP631 IS AN INTERCALATOR' 2 non-polymer syn '4-METHYLBENZYL-N-BIS[DAUNOMYCIN]' 1159.189 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DT)' _entity_poly.pdbx_seq_one_letter_code_can ACGTACGT _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # 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 DG n 1 4 DT n 1 5 DA n 1 6 DC n 1 7 DG n 1 8 DT n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1AL9 _struct_ref.pdbx_db_accession 1AL9 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1AL9 A 1 ? 8 ? 1AL9 1 ? 8 ? 1 8 2 1 1AL9 B 1 ? 8 ? 1AL9 9 ? 16 ? 9 16 # 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 BDA non-polymer . '4-METHYLBENZYL-N-BIS[DAUNOMYCIN]' WP631 'C62 H66 N2 O20 2' 1159.189 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 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 TOCSY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 275 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'INOVA 750' _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 750 # _pdbx_nmr_refine.entry_id 1AL9 _pdbx_nmr_refine.method NOE-RMD _pdbx_nmr_refine.details 'REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1AL9 _pdbx_nmr_details.text 'IONIC_STRENGTH: 20 MM PRESSURE: NULL SOLVENT SYSTEM: H2O' # _pdbx_nmr_ensemble.entry_id 1AL9 _pdbx_nmr_ensemble.conformers_calculated_total_number 1 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'MINIMIZED AVERAGE' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR ? BRUNGER 1 'structure solution' X-PLOR ? ? 2 'structure solution' SPEDREF ? ? 3 # _exptl.entry_id 1AL9 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1AL9 _struct.title ;NMR STUDY OF DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3') SELF-COMPLEMENTARY DUPLEX COMPLEXED WITH A BIS-DAUNORUBICIN, MINIMIZED AVERAGE STRUCTURE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1AL9 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'COMPLEX (DEOXYRIBONUCLEIC ACID-DRUG), BIS-INTERCALATOR, DAUNORUBICIN, DNA, DEOXYRIBONUCLEIC ACID' # 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 ? # _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 hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 1 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 1 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 4 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 4 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 5 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 5 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 7 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 7 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 7 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 8 B DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 8 B DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id BDA _struct_site.pdbx_auth_seq_id 17 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 12 _struct_site.details 'BINDING SITE FOR RESIDUE BDA A 17' # 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 12 DC A 2 ? DC A 2 . ? 1_555 ? 2 AC1 12 DG A 3 ? DG A 3 . ? 1_555 ? 3 AC1 12 DT A 4 ? DT A 4 . ? 1_555 ? 4 AC1 12 DA A 5 ? DA A 5 . ? 1_555 ? 5 AC1 12 DC A 6 ? DC A 6 . ? 1_555 ? 6 AC1 12 DG A 7 ? DG A 7 . ? 1_555 ? 7 AC1 12 DC B 2 ? DC B 10 . ? 1_555 ? 8 AC1 12 DG B 3 ? DG B 11 . ? 1_555 ? 9 AC1 12 DT B 4 ? DT B 12 . ? 1_555 ? 10 AC1 12 DA B 5 ? DA B 13 . ? 1_555 ? 11 AC1 12 DC B 6 ? DC B 14 . ? 1_555 ? 12 AC1 12 DG B 7 ? DG B 15 . ? 1_555 ? # _database_PDB_matrix.entry_id 1AL9 _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 1AL9 _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 DA 1 1 1 DA A A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T 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 DT 8 8 8 DT T A . n B 1 1 DA 1 9 9 DA A B . n B 1 2 DC 2 10 10 DC C B . n B 1 3 DG 3 11 11 DG G B . n B 1 4 DT 4 12 12 DT T B . n B 1 5 DA 5 13 13 DA A B . n B 1 6 DC 6 14 14 DC C B . n B 1 7 DG 7 15 15 DG G B . n B 1 8 DT 8 16 16 DT T B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id BDA _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 17 _pdbx_nonpoly_scheme.auth_seq_num 17 _pdbx_nonpoly_scheme.pdb_mon_id BDA _pdbx_nonpoly_scheme.auth_mon_id DM1 _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 1997-09-17 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_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_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C5 _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DT _pdbx_validate_rmsd_bond.auth_seq_id_1 12 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 C7 _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DT _pdbx_validate_rmsd_bond.auth_seq_id_2 12 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.533 _pdbx_validate_rmsd_bond.bond_target_value 1.496 _pdbx_validate_rmsd_bond.bond_deviation 0.037 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag 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 DA 1 ? ? "C4'" A DA 1 ? ? "C3'" A DA 1 ? ? 110.48 106.00 4.48 0.60 N 2 1 "O4'" A DA 1 ? ? "C1'" A DA 1 ? ? N9 A DA 1 ? ? 102.98 108.00 -5.02 0.70 N 3 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? "C2'" A DC 2 ? ? 100.75 105.90 -5.15 0.80 N 4 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 113.10 108.30 4.80 0.30 N 5 1 "O4'" A DG 3 ? ? "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? 109.63 106.00 3.63 0.60 N 6 1 C8 A DG 3 ? ? N9 A DG 3 ? ? C4 A DG 3 ? ? 103.89 106.40 -2.51 0.40 N 7 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 112.64 108.30 4.34 0.30 N 8 1 "C4'" A DA 5 ? ? "C3'" A DA 5 ? ? "C2'" A DA 5 ? ? 97.83 102.20 -4.37 0.70 N 9 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 110.59 108.30 2.29 0.30 N 10 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 110.93 108.30 2.63 0.30 N 11 1 "O4'" A DG 7 ? ? "C4'" A DG 7 ? ? "C3'" A DG 7 ? ? 111.26 106.00 5.26 0.60 N 12 1 C6 A DT 8 ? ? C5 A DT 8 ? ? C7 A DT 8 ? ? 117.65 122.90 -5.25 0.60 N 13 1 "O4'" B DA 9 ? ? "C4'" B DA 9 ? ? "C3'" B DA 9 ? ? 110.52 106.00 4.52 0.60 N 14 1 "O4'" B DA 9 ? ? "C1'" B DA 9 ? ? N9 B DA 9 ? ? 103.05 108.00 -4.95 0.70 N 15 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? "C2'" B DC 10 ? ? 100.76 105.90 -5.14 0.80 N 16 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? N1 B DC 10 ? ? 113.15 108.30 4.85 0.30 N 17 1 "O4'" B DG 11 ? ? "C4'" B DG 11 ? ? "C3'" B DG 11 ? ? 109.72 106.00 3.72 0.60 N 18 1 C8 B DG 11 ? ? N9 B DG 11 ? ? C4 B DG 11 ? ? 103.92 106.40 -2.48 0.40 N 19 1 "O4'" B DT 12 ? ? "C1'" B DT 12 ? ? N1 B DT 12 ? ? 112.39 108.30 4.09 0.30 N 20 1 "C4'" B DA 13 ? ? "C3'" B DA 13 ? ? "C2'" B DA 13 ? ? 97.76 102.20 -4.44 0.70 N 21 1 "O4'" B DA 13 ? ? "C1'" B DA 13 ? ? N9 B DA 13 ? ? 110.61 108.30 2.31 0.30 N 22 1 "O4'" B DC 14 ? ? "C1'" B DC 14 ? ? N1 B DC 14 ? ? 110.92 108.30 2.62 0.30 N 23 1 "O4'" B DG 15 ? ? "C4'" B DG 15 ? ? "C3'" B DG 15 ? ? 110.85 106.00 4.85 0.60 N 24 1 C6 B DT 16 ? ? C5 B DT 16 ? ? C7 B DT 16 ? ? 119.11 122.90 -3.79 0.60 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 DT A 4 ? ? 0.085 'SIDE CHAIN' 2 1 DC A 6 ? ? 0.092 'SIDE CHAIN' 3 1 DT B 12 ? ? 0.085 'SIDE CHAIN' 4 1 DC B 14 ? ? 0.092 'SIDE CHAIN' # _ndb_struct_conf_na.entry_id 1AL9 _ndb_struct_conf_na.feature '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 0.255 -0.022 0.453 5.149 3.767 8.773 1 A_DA1:DT16_B A 1 ? B 16 ? 20 1 1 A DC 2 1_555 B DG 7 1_555 0.587 -0.276 -0.035 13.971 -6.261 -6.375 2 A_DC2:DG15_B A 2 ? B 15 ? 19 1 1 A DG 3 1_555 B DC 6 1_555 -0.482 -0.124 -0.324 -18.129 9.481 4.370 3 A_DG3:DC14_B A 3 ? B 14 ? 19 1 1 A DT 4 1_555 B DA 5 1_555 -0.083 -0.067 0.312 -6.360 -11.052 -1.813 4 A_DT4:DA13_B A 4 ? B 13 ? 20 1 1 A DA 5 1_555 B DT 4 1_555 0.086 -0.074 0.320 6.429 -11.165 -1.893 5 A_DA5:DT12_B A 5 ? B 12 ? 20 1 1 A DC 6 1_555 B DG 3 1_555 0.483 -0.133 -0.322 18.184 9.451 4.374 6 A_DC6:DG11_B A 6 ? B 11 ? 19 1 1 A DG 7 1_555 B DC 2 1_555 -0.600 -0.286 -0.033 -13.983 -6.332 -6.295 7 A_DG7:DC10_B A 7 ? B 10 ? 19 1 1 A DT 8 1_555 B DA 1 1_555 -0.268 -0.021 0.459 -5.284 3.881 8.955 8 A_DT8:DA9_B A 8 ? B 9 ? 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 -0.191 -0.320 3.105 5.499 -5.668 29.907 0.448 1.375 3.031 -10.749 -10.428 30.909 1 AA_DA1DC2:DG15DT16_BB A 1 ? B 16 ? A 2 ? B 15 ? 1 A DC 2 1_555 B DG 7 1_555 A DG 3 1_555 B DC 6 1_555 1.037 0.611 6.947 2.263 -4.715 35.292 2.448 -0.997 6.862 -7.724 -3.707 35.666 2 AA_DC2DG3:DC14DG15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A DG 3 1_555 B DC 6 1_555 A DT 4 1_555 B DA 5 1_555 -0.910 -0.367 2.980 -4.904 -1.150 27.543 -0.504 0.792 3.105 -2.390 10.191 27.991 3 AA_DG3DT4:DA13DC14_BB A 3 ? B 14 ? A 4 ? B 13 ? 1 A DT 4 1_555 B DA 5 1_555 A DA 5 1_555 B DT 4 1_555 -0.002 0.979 3.464 -0.103 10.217 34.487 -0.024 -0.013 3.600 16.783 0.170 35.924 4 AA_DT4DA5:DT12DA13_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A DA 5 1_555 B DT 4 1_555 A DC 6 1_555 B DG 3 1_555 0.911 -0.368 2.981 4.985 -1.208 27.558 -0.492 -0.775 3.107 -2.508 -10.351 28.023 5 AA_DA5DC6:DG11DT12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A DC 6 1_555 B DG 3 1_555 A DG 7 1_555 B DC 2 1_555 -1.036 0.611 6.948 -2.267 -4.722 35.318 2.448 0.994 6.863 -7.730 3.711 35.692 6 AA_DC6DG7:DC10DG11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A DG 7 1_555 B DC 2 1_555 A DT 8 1_555 B DA 1 1_555 0.191 -0.320 3.106 -5.586 -5.593 29.964 0.431 -1.388 3.031 -10.588 10.574 30.966 7 AA_DG7DT8:DA9DC10_BB A 7 ? B 10 ? A 8 ? B 9 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name '4-METHYLBENZYL-N-BIS[DAUNOMYCIN]' _pdbx_entity_nonpoly.comp_id BDA #