data_107D # _entry.id 107D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 107D pdb_0000107d 10.2210/pdb107d/pdb WWPDB D_1000170017 ? ? # 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 1995-05-08 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 5 'Structure model' 1 4 2024-03-13 # _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 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Source and taxonomy' 8 5 'Structure model' 'Structure summary' # 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 6 5 'Structure model' chem_comp_atom 7 5 'Structure model' chem_comp_bond 8 5 'Structure model' entity 9 5 'Structure model' pdbx_entity_src_syn # 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' 7 5 'Structure model' '_entity.details' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 107D _pdbx_database_status.recvd_initial_deposition_date 1995-01-17 _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.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 'Lin, C.H.' 1 'Patel, D.J.' 2 # _citation.id primary _citation.title 'Solution structure of the covalent duocarmycin A-DNA duplex complex.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 248 _citation.page_first 162 _citation.page_last 179 _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 7731041 _citation.pdbx_database_id_DOI 10.1006/jmbi.1995.0209 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lin, C.H.' 1 ? primary 'Patel, D.J.' 2 ? # 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(*CP*CP*TP*TP*TP*TP*C)-3') ; 2039.359 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3') ; 2195.487 1 ? ? ? ? 3 non-polymer syn ;4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER ; 509.508 1 ? ? ? 'CHEMICALLY SYNTHESIZED' # loop_ _entity_keywords.entity_id _entity_keywords.text 1 'DEOXYRIBONUCLEIC ACID' 2 'DEOXYRIBONUCLEIC ACID' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DC)(DC)(DT)(DT)(DT)(DT)(DC)' CCTTTTC A ? 2 polydeoxyribonucleotide no no '(DG)(DA)(DA)(DA)(DA)(DG)(DG)' GAAAAGG B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name ;4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER ; _pdbx_entity_nonpoly.comp_id DUO # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DT n 1 4 DT n 1 5 DT n 1 6 DT n 1 7 DC n 2 1 DG n 2 2 DA n 2 3 DA n 2 4 DA n 2 5 DA n 2 6 DG n 2 7 DG n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? 'CHEMICALLY SYNTHESIZED' 2 1 sample ? ? ? ? ? 'CHEMICALLY SYNTHESIZED' # 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 DUO non-polymer . ;4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER ; 'DUOCARMYCIN A' 'C26 H27 N3 O8' 509.508 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DC 7 7 7 DC C A . n B 2 1 DG 1 8 8 DG G B . n B 2 2 DA 2 9 9 DA A B . n B 2 3 DA 3 10 10 DA A B . n B 2 4 DA 4 11 11 DA A B . n B 2 5 DA 5 12 12 DA A B . n B 2 6 DG 6 13 13 DG G B . n B 2 7 DG 7 14 14 DG G B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id DUO _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 15 _pdbx_nonpoly_scheme.auth_seq_num 15 _pdbx_nonpoly_scheme.pdb_mon_id DUO _pdbx_nonpoly_scheme.auth_mon_id DUO _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.pdb_ins_code . # 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 # _cell.entry_id 107D _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 107D _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 107D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 107D _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 # _struct.entry_id 107D _struct.title 'SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 107D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, DOUBLE HELIX' # 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 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 PDB 107D 107D ? ? ? 2 2 PDB 107D 107D ? ? ? # 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 107D A 1 ? 7 ? 107D 1 ? 7 ? 1 7 2 2 107D B 1 ? 7 ? 107D 8 ? 14 ? 8 14 # _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 # _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 hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 1 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 2 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 3 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 3 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 4 B DA 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 4 B DA 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 5 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 5 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 6 B DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 6 B DA 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 7 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 7 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 7 B DG 8 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 B _struct_site.pdbx_auth_comp_id DUO _struct_site.pdbx_auth_seq_id 15 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'BINDING SITE FOR RESIDUE DUO B 15' # 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 9 DT A 4 ? DT A 4 . ? 1_555 ? 2 AC1 9 DT A 5 ? DT A 5 . ? 1_555 ? 3 AC1 9 DT A 6 ? DT A 6 . ? 1_555 ? 4 AC1 9 DC A 7 ? DC A 7 . ? 1_555 ? 5 AC1 9 DA B 3 ? DA B 10 . ? 1_555 ? 6 AC1 9 DA B 4 ? DA B 11 . ? 1_555 ? 7 AC1 9 DA B 5 ? DA B 12 . ? 1_555 ? 8 AC1 9 DG B 6 ? DG B 13 . ? 1_555 ? 9 AC1 9 DG B 7 ? DG B 14 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 N3 B DA 12 ? ? C10 B DUO 15 ? ? 1.41 2 2 N3 B DA 12 ? ? C10 B DUO 15 ? ? 1.41 3 3 N3 B DA 12 ? ? C10 B DUO 15 ? ? 1.41 4 4 N3 B DA 12 ? ? C10 B DUO 15 ? ? 1.40 # 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 C5 A DT 5 ? ? C7 A DT 5 ? ? 1.537 1.496 0.041 0.006 N 2 2 C5 A DT 3 ? ? C7 A DT 3 ? ? 1.534 1.496 0.038 0.006 N 3 2 C5 A DT 4 ? ? C7 A DT 4 ? ? 1.533 1.496 0.037 0.006 N 4 2 C5 A DT 5 ? ? C7 A DT 5 ? ? 1.544 1.496 0.048 0.006 N 5 2 C5 A DT 6 ? ? C7 A DT 6 ? ? 1.532 1.496 0.036 0.006 N 6 4 C5 A DT 3 ? ? C7 A DT 3 ? ? 1.536 1.496 0.040 0.006 N 7 4 C5 A DT 5 ? ? C7 A DT 5 ? ? 1.535 1.496 0.039 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 DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.36 105.90 -5.54 0.80 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 117.65 108.30 9.35 0.30 N 3 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 122.85 118.90 3.95 0.60 N 4 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 113.40 108.30 5.10 0.30 N 5 1 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.24 122.90 -3.66 0.60 N 6 1 "C5'" A DT 4 ? ? "C4'" A DT 4 ? ? "O4'" A DT 4 ? ? 118.34 109.80 8.54 1.10 N 7 1 N3 A DT 4 ? ? C2 A DT 4 ? ? O2 A DT 4 ? ? 118.65 122.30 -3.65 0.60 N 8 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 118.95 122.90 -3.95 0.60 N 9 1 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 119.11 122.90 -3.79 0.60 N 10 1 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 110.50 108.30 2.20 0.30 N 11 1 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 118.94 122.90 -3.96 0.60 N 12 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 110.15 108.30 1.85 0.30 N 13 1 "O4'" B DA 10 ? ? "C1'" B DA 10 ? ? N9 B DA 10 ? ? 113.47 108.30 5.17 0.30 N 14 1 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? "C2'" B DA 12 ? ? 100.72 105.90 -5.18 0.80 N 15 1 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 114.19 108.30 5.89 0.30 N 16 1 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DG 14 ? ? 128.16 119.70 8.46 1.20 Y 17 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 114.25 108.30 5.95 0.30 N 18 2 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.74 105.90 -5.16 0.80 N 19 2 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.70 108.30 4.40 0.30 N 20 2 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 109.77 106.00 3.77 0.60 N 21 2 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 123.14 118.90 4.24 0.60 N 22 2 "C3'" A DT 3 ? ? "O3'" A DT 3 ? ? P A DT 4 ? ? 127.24 119.70 7.54 1.20 Y 23 2 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 119.18 122.90 -3.72 0.60 N 24 2 "O4'" B DA 10 ? ? "C1'" B DA 10 ? ? N9 B DA 10 ? ? 112.12 108.30 3.82 0.30 N 25 2 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 114.05 108.30 5.75 0.30 N 26 2 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DG 14 ? ? 127.77 119.70 8.07 1.20 Y 27 2 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 112.65 108.30 4.35 0.30 N 28 3 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.63 105.90 -5.27 0.80 N 29 3 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 118.24 108.30 9.94 0.30 N 30 3 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 122.53 118.90 3.63 0.60 N 31 3 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 111.04 108.30 2.74 0.30 N 32 3 "C5'" A DT 4 ? ? "C4'" A DT 4 ? ? "O4'" A DT 4 ? ? 117.23 109.80 7.43 1.10 N 33 3 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 118.96 122.90 -3.94 0.60 N 34 3 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 110.15 108.30 1.85 0.30 N 35 3 "O4'" B DA 10 ? ? "C1'" B DA 10 ? ? N9 B DA 10 ? ? 111.39 108.30 3.09 0.30 N 36 3 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? "C2'" B DA 12 ? ? 99.47 105.90 -6.43 0.80 N 37 3 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 114.43 108.30 6.13 0.30 N 38 3 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DG 14 ? ? 128.67 119.70 8.97 1.20 Y 39 3 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 113.65 108.30 5.35 0.30 N 40 4 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.96 105.90 -4.94 0.80 N 41 4 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.76 108.30 4.46 0.30 N 42 4 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 109.69 106.00 3.69 0.60 N 43 4 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 123.08 118.90 4.18 0.60 N 44 4 "C3'" A DT 3 ? ? "O3'" A DT 3 ? ? P A DT 4 ? ? 127.59 119.70 7.89 1.20 Y 45 4 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 119.13 122.90 -3.77 0.60 N 46 4 N1 A DC 7 ? ? C2 A DC 7 ? ? O2 A DC 7 ? ? 122.73 118.90 3.83 0.60 N 47 4 "C3'" B DG 8 ? ? "O3'" B DG 8 ? ? P B DA 9 ? ? 127.86 119.70 8.16 1.20 Y 48 4 "O4'" B DA 9 ? ? "C1'" B DA 9 ? ? N9 B DA 9 ? ? 114.53 108.30 6.23 0.30 N 49 4 "C3'" B DA 9 ? ? "O3'" B DA 9 ? ? P B DA 10 ? ? 127.49 119.70 7.79 1.20 Y 50 4 "O4'" B DA 10 ? ? "C1'" B DA 10 ? ? N9 B DA 10 ? ? 114.50 108.30 6.20 0.30 N 51 4 "C4'" B DA 12 ? ? "C3'" B DA 12 ? ? "C2'" B DA 12 ? ? 97.88 102.20 -4.32 0.70 N 52 4 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? "C2'" B DA 12 ? ? 100.09 105.90 -5.81 0.80 N 53 4 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 110.54 108.30 2.24 0.30 N 54 4 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DG 14 ? ? 127.62 119.70 7.92 1.20 Y 55 4 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 112.40 108.30 4.10 0.30 N # _pdbx_nmr_ensemble.entry_id 107D _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 4 _pdbx_nmr_ensemble.conformer_selection_criteria ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_details.entry_id 107D _pdbx_nmr_details.text 'DUOCARMYCIN A WAS PROVIDED BY KYOWA HAKKO KOGYO CO., JAPAN.' # _pdbx_nmr_refine.entry_id 107D _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 2-D NMR DATA. ONE INITIAL VELOCITY SEED WAS USED FOR EACH STARTING STRUCTURE WHICH YIELDS TWO DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER WITH TWO INITIAL VELOCITIES USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS TO GENERATE THE FINAL FOUR STRUCTURES. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.0 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 40, 80, 120 AND 160 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1-MODEL4 R(1/6) FACTOR 0.042-0.045 BOND (ANG) 0.009-0.010 ANGLES (DEG) 3.078-3.780 IMPROPERS (DEG) 0.310-0.321. THE STRUCTURE HAS APPROXIMATE TWO-FOLD SYMMETRY RELATING THE TWO STRANDS OF THE DNA WITH THE SYMMETRY AXIS PERPENDICULAR TO THE HELICAL AXIS. THE TRANSFORMATION MATRIX WAS CALCULATED FOR THE AVERAGED STRUCTURE OF THE FOUR MODELS. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_software.name X-PLOR _pdbx_nmr_software.version ? _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors BRUNGER _pdbx_nmr_software.ordinal 1 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 DUO N1 N N N 144 DUO C2 C N R 145 DUO C3 C N N 146 DUO C4 C Y N 147 DUO C5 C Y N 148 DUO C6 C Y N 149 DUO C7 C Y N 150 DUO C8 C Y N 151 DUO C9 C Y N 152 DUO C10 C N N 153 DUO C11 C N S 154 DUO C12 C N N 155 DUO N13 N N N 156 DUO C14 C N N 157 DUO C15 C Y N 158 DUO C16 C Y N 159 DUO C17 C Y N 160 DUO C18 C Y N 161 DUO C19 C Y N 162 DUO C20 C Y N 163 DUO C21 C Y N 164 DUO C22 C Y N 165 DUO N23 N Y N 166 DUO O24 O N N 167 DUO C25 C N N 168 DUO O26 O N N 169 DUO C27 C N N 170 DUO O28 O N N 171 DUO C29 C N N 172 DUO O30 O N N 173 DUO O31 O N N 174 DUO O32 O N N 175 DUO C33 C N N 176 DUO C34 C N N 177 DUO O35 O N N 178 DUO O36 O N N 179 DUO C37 C N N 180 DUO H1 H N N 181 DUO H7 H N N 182 DUO H101 H N N 183 DUO H102 H N N 184 DUO H103 H N N 185 DUO H11 H N N 186 DUO H121 H N N 187 DUO H122 H N N 188 DUO H16 H N N 189 DUO H18 H N N 190 DUO H23 H N N 191 DUO H251 H N N 192 DUO H252 H N N 193 DUO H253 H N N 194 DUO H271 H N N 195 DUO H272 H N N 196 DUO H273 H N N 197 DUO H291 H N N 198 DUO H292 H N N 199 DUO H293 H N N 200 DUO H31 H N N 201 DUO H331 H N N 202 DUO H332 H N N 203 DUO H333 H N N 204 DUO H371 H N N 205 DUO H372 H N N 206 DUO H373 H N N 207 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 DUO N1 C2 sing N N 150 DUO N1 C5 sing N N 151 DUO N1 H1 sing N N 152 DUO C2 C3 sing N N 153 DUO C2 C33 sing N N 154 DUO C2 C34 sing N N 155 DUO C3 C4 sing N N 156 DUO C3 O32 doub N N 157 DUO C4 C5 doub Y N 158 DUO C4 C9 sing Y N 159 DUO C5 C6 sing Y N 160 DUO C6 C7 doub Y N 161 DUO C6 O31 sing N N 162 DUO C7 C8 sing Y N 163 DUO C7 H7 sing N N 164 DUO C8 C9 doub Y N 165 DUO C8 N13 sing N N 166 DUO C9 C11 sing N N 167 DUO C10 C11 sing N N 168 DUO C10 H101 sing N N 169 DUO C10 H102 sing N N 170 DUO C10 H103 sing N N 171 DUO C11 C12 sing N N 172 DUO C11 H11 sing N N 173 DUO C12 N13 sing N N 174 DUO C12 H121 sing N N 175 DUO C12 H122 sing N N 176 DUO N13 C14 sing N N 177 DUO C14 C15 sing N N 178 DUO C14 O30 doub N N 179 DUO C15 C16 doub Y N 180 DUO C15 N23 sing Y N 181 DUO C16 C17 sing Y N 182 DUO C16 H16 sing N N 183 DUO C17 C18 doub Y N 184 DUO C17 C22 sing Y N 185 DUO C18 C19 sing Y N 186 DUO C18 H18 sing N N 187 DUO C19 C20 doub Y N 188 DUO C19 O24 sing N N 189 DUO C20 C21 sing Y N 190 DUO C20 O26 sing N N 191 DUO C21 C22 doub Y N 192 DUO C21 O28 sing N N 193 DUO C22 N23 sing Y N 194 DUO N23 H23 sing N N 195 DUO O24 C25 sing N N 196 DUO C25 H251 sing N N 197 DUO C25 H252 sing N N 198 DUO C25 H253 sing N N 199 DUO O26 C27 sing N N 200 DUO C27 H271 sing N N 201 DUO C27 H272 sing N N 202 DUO C27 H273 sing N N 203 DUO O28 C29 sing N N 204 DUO C29 H291 sing N N 205 DUO C29 H292 sing N N 206 DUO C29 H293 sing N N 207 DUO O31 H31 sing N N 208 DUO C33 H331 sing N N 209 DUO C33 H332 sing N N 210 DUO C33 H333 sing N N 211 DUO C34 O35 doub N N 212 DUO C34 O36 sing N N 213 DUO O36 C37 sing N N 214 DUO C37 H371 sing N N 215 DUO C37 H372 sing N N 216 DUO C37 H373 sing N N 217 # _ndb_struct_conf_na.entry_id 107D _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 DC 1 1_555 B DG 7 1_555 0.473 -0.264 -0.285 3.839 -3.256 -0.998 1 A_DC1:DG14_B A 1 ? B 14 ? 19 1 1 A DC 2 1_555 B DG 6 1_555 0.466 -0.220 -0.032 -1.193 -6.733 -2.815 2 A_DC2:DG13_B A 2 ? B 13 ? 19 1 1 A DT 3 1_555 B DA 5 1_555 -0.679 0.151 -0.275 2.465 -14.247 -9.859 3 A_DT3:DA12_B A 3 ? B 12 ? 20 1 1 A DT 4 1_555 B DA 4 1_555 -0.233 -0.117 -0.064 7.883 -27.323 6.447 4 A_DT4:DA11_B A 4 ? B 11 ? 20 1 1 A DT 5 1_555 B DA 3 1_555 -0.126 -0.207 -0.100 -3.567 -26.784 7.911 5 A_DT5:DA10_B A 5 ? B 10 ? 20 1 1 A DT 6 1_555 B DA 2 1_555 0.217 -0.131 0.212 -4.502 -6.098 -4.255 6 A_DT6:DA9_B A 6 ? B 9 ? 20 1 1 A DC 7 1_555 B DG 1 1_555 0.738 -0.307 -0.343 5.168 -10.630 -0.701 7 A_DC7:DG8_B A 7 ? B 8 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 7 1_555 A DC 2 1_555 B DG 6 1_555 -1.346 -0.311 3.455 -3.521 -0.926 37.246 -0.354 1.601 3.569 -1.446 5.497 37.417 1 AA_DC1DC2:DG13DG14_BB A 1 ? B 14 ? A 2 ? B 13 ? 1 A DC 2 1_555 B DG 6 1_555 A DT 3 1_555 B DA 5 1_555 0.360 1.543 3.278 6.643 -0.783 30.874 2.983 0.582 3.243 -1.450 -12.297 31.573 2 AA_DC2DT3:DA12DG13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A DT 3 1_555 B DA 5 1_555 A DT 4 1_555 B DA 4 1_555 0.726 -0.148 2.871 -0.712 2.089 33.808 -0.548 -1.347 2.841 3.588 1.222 33.878 3 AA_DT3DT4:DA11DA12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A DT 4 1_555 B DA 4 1_555 A DT 5 1_555 B DA 3 1_555 0.440 0.652 3.313 6.797 -3.434 42.674 1.223 0.077 3.283 -4.675 -9.252 43.317 4 AA_DT4DT5:DA10DA11_BB A 4 ? B 11 ? A 5 ? B 10 ? 1 A DT 5 1_555 B DA 3 1_555 A DT 6 1_555 B DA 2 1_555 -0.207 -0.127 3.157 -1.785 0.788 33.587 -0.344 0.076 3.160 1.362 3.085 33.642 5 AA_DT5DT6:DA9DA10_BB A 5 ? B 10 ? A 6 ? B 9 ? 1 A DT 6 1_555 B DA 2 1_555 A DC 7 1_555 B DG 1 1_555 1.084 0.046 2.847 6.945 -0.551 40.626 0.119 -0.868 2.984 -0.786 -9.914 41.194 6 AA_DT6DC7:DG8DA9_BB A 6 ? B 9 ? A 7 ? B 8 ? # _atom_sites.entry_id 107D _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_