data_202D # _entry.id 202D # _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 202D pdb_0000202d 10.2210/pdb202d/pdb WWPDB D_1000177553 ? ? # 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 1995-06-03 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 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 202D _pdbx_database_status.recvd_initial_deposition_date 1995-03-29 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Chen, H.' 1 'Patel, D.J.' 2 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Solution Structure of the Menogaril-DNA Complex' J.Am.Chem.Soc. 117 5901 5913 1995 JACSAT US 0002-7863 0004 ? -1 ? 1 'Antitumor Drug Nogalamycin Binds DNA in Both Grooves Simultaneously: Molecular Structure of Nogalamycin-DNA Complex' Biochemistry 28 9913 ? 1989 BICHAW US 0006-2960 0033 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chen, H.' 1 ? primary 'Patel, D.J.' 2 ? 1 'Liaw, Y.-C.' 3 ? 1 'Gao, Y.-G.' 4 ? 1 'Robinson, H.' 5 ? 1 'Van Der Marel, G.A.' 6 ? 1 'Van Boom, J.H.' 7 ? 1 'Wang, A.H.' 8 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*GP*AP*CP*AP*TP*GP*TP*C)-3') ; 2426.617 2 ? ? ? ? 2 non-polymer syn MENOGARIL 541.546 2 ? ? ? 'CHEMICALLY SYNTHESIZED' # _entity_keywords.entity_id 1 _entity_keywords.text 'DEOXYRIBONUCLEIC ACID' # _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 '(DG)(DA)(DC)(DA)(DT)(DG)(DT)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GACATGTC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name MENOGARIL _pdbx_entity_nonpoly.comp_id MNG # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DA n 1 3 DC n 1 4 DA n 1 5 DT n 1 6 DG n 1 7 DT n 1 8 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _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 '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 MNG non-polymer . MENOGARIL ? 'C28 H31 N O10' 541.546 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DA 2 2 2 DA A A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DC 8 8 8 DC C A . n B 1 1 DG 1 1 1 DG G B . n B 1 2 DA 2 2 2 DA A B . n B 1 3 DC 3 3 3 DC C B . n B 1 4 DA 4 4 4 DA A B . n B 1 5 DT 5 5 5 DT T B . n B 1 6 DG 6 6 6 DG G B . n B 1 7 DT 7 7 7 DT T B . n B 1 8 DC 8 8 8 DC C B . 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 C 2 MNG 1 9 2 MNG MNG A . D 2 MNG 1 9 1 MNG MNG B . # _cell.entry_id 202D _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 202D _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 202D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 202D _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 202D _struct.title 'SOLUTION STRUCTURE OF THE MENOGARIL-DNA COMPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 202D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, MENOGARIL' # 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 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 202D _struct_ref.pdbx_db_accession 202D _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 202D A 1 ? 8 ? 202D 1 ? 8 ? 1 8 2 1 202D B 1 ? 8 ? 202D 1 ? 8 ? 1 8 # _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,D # _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 # 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 DG 1 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 2 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 2 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 3 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 3 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 3 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 4 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 4 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 5 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 5 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 6 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 6 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 6 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 7 B DA 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 7 B DA 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _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 _struct_site.details AC1 Software B MNG 9 ? 5 'BINDING SITE FOR RESIDUE MNG B 9' AC2 Software A MNG 9 ? 5 'BINDING SITE FOR RESIDUE MNG A 9' # 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 5 DC A 3 ? DC A 3 . ? 1_555 ? 2 AC1 5 DA A 4 ? DA A 4 . ? 1_555 ? 3 AC1 5 DT B 5 ? DT B 5 . ? 1_555 ? 4 AC1 5 DG B 6 ? DG B 6 . ? 1_555 ? 5 AC1 5 DT B 7 ? DT B 7 . ? 1_555 ? 6 AC2 5 DT A 5 ? DT A 5 . ? 1_555 ? 7 AC2 5 DG A 6 ? DG A 6 . ? 1_555 ? 8 AC2 5 DT A 7 ? DT A 7 . ? 1_555 ? 9 AC2 5 DC B 3 ? DC B 3 . ? 1_555 ? 10 AC2 5 DA B 4 ? DA B 4 . ? 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 H21 A DG 6 ? ? O2 B DC 3 ? ? 1.57 2 1 OP1 A DT 7 ? ? HO9 A MNG 9 ? ? 1.57 3 1 O2 A DC 3 ? ? H21 B DG 6 ? ? 1.58 4 2 OP1 A DT 7 ? ? HO9 A MNG 9 ? ? 1.56 5 2 H21 A DG 6 ? ? O2 B DC 3 ? ? 1.56 6 2 OP1 B DT 7 ? ? HO9 B MNG 9 ? ? 1.57 7 2 O2 A DC 3 ? ? H21 B DG 6 ? ? 1.58 8 3 OP1 B DT 7 ? ? HO9 B MNG 9 ? ? 1.58 9 3 O2 A DC 3 ? ? H21 B DG 6 ? ? 1.59 10 3 H21 A DG 6 ? ? O2 B DC 3 ? ? 1.59 # 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 2 C5 A DT 7 ? ? C7 A DT 7 ? ? 1.533 1.496 0.037 0.006 N 2 2 C5 B DT 7 ? ? C7 B DT 7 ? ? 1.533 1.496 0.037 0.006 N 3 3 C5 A DT 7 ? ? C7 A DT 7 ? ? 1.533 1.496 0.037 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 N7 A DG 1 ? ? C8 A DG 1 ? ? N9 A DG 1 ? ? 116.30 113.10 3.20 0.50 N 2 1 N7 A DA 2 ? ? C8 A DA 2 ? ? N9 A DA 2 ? ? 117.20 113.80 3.40 0.50 N 3 1 C8 A DA 2 ? ? N9 A DA 2 ? ? C4 A DA 2 ? ? 103.38 105.80 -2.42 0.40 N 4 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 101.44 108.00 -6.56 0.70 N 5 1 "O4'" A DA 4 ? ? "C4'" A DA 4 ? ? "C3'" A DA 4 ? ? 110.11 106.00 4.11 0.60 N 6 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.97 108.30 4.67 0.30 N 7 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.18 108.30 1.88 0.30 N 8 1 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.04 122.90 -4.86 0.60 N 9 1 "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? "O4'" A DG 6 ? ? 117.77 109.80 7.97 1.10 N 10 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? "C2'" A DG 6 ? ? 100.72 105.90 -5.18 0.80 N 11 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 111.74 108.30 3.44 0.30 N 12 1 N7 A DG 6 ? ? C8 A DG 6 ? ? N9 A DG 6 ? ? 116.52 113.10 3.42 0.50 N 13 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? "C2'" A DT 7 ? ? 100.58 105.90 -5.32 0.80 N 14 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 114.35 108.30 6.05 0.30 N 15 1 "C5'" A DC 8 ? ? "C4'" A DC 8 ? ? "O4'" A DC 8 ? ? 116.71 109.80 6.91 1.10 N 16 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.68 108.30 2.38 0.30 N 17 1 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 122.72 118.90 3.82 0.60 N 18 1 N7 B DG 1 ? ? C8 B DG 1 ? ? N9 B DG 1 ? ? 116.38 113.10 3.28 0.50 N 19 1 N7 B DA 2 ? ? C8 B DA 2 ? ? N9 B DA 2 ? ? 117.23 113.80 3.43 0.50 N 20 1 C8 B DA 2 ? ? N9 B DA 2 ? ? C4 B DA 2 ? ? 103.34 105.80 -2.46 0.40 N 21 1 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 101.53 108.00 -6.47 0.70 N 22 1 "O4'" B DA 4 ? ? "C4'" B DA 4 ? ? "C3'" B DA 4 ? ? 110.04 106.00 4.04 0.60 N 23 1 "O4'" B DA 4 ? ? "C1'" B DA 4 ? ? N9 B DA 4 ? ? 113.14 108.30 4.84 0.30 N 24 1 C6 B DT 5 ? ? C5 B DT 5 ? ? C7 B DT 5 ? ? 117.92 122.90 -4.98 0.60 N 25 1 "C5'" B DG 6 ? ? "C4'" B DG 6 ? ? "O4'" B DG 6 ? ? 117.81 109.80 8.01 1.10 N 26 1 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? "C2'" B DG 6 ? ? 100.72 105.90 -5.18 0.80 N 27 1 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? N9 B DG 6 ? ? 111.68 108.30 3.38 0.30 N 28 1 N7 B DG 6 ? ? C8 B DG 6 ? ? N9 B DG 6 ? ? 116.59 113.10 3.49 0.50 N 29 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? "C2'" B DT 7 ? ? 100.74 105.90 -5.16 0.80 N 30 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 114.32 108.30 6.02 0.30 N 31 1 "C5'" B DC 8 ? ? "C4'" B DC 8 ? ? "O4'" B DC 8 ? ? 116.67 109.80 6.87 1.10 N 32 1 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 110.73 108.30 2.43 0.30 N 33 1 N1 B DC 8 ? ? C2 B DC 8 ? ? O2 B DC 8 ? ? 122.81 118.90 3.91 0.60 N 34 2 N7 A DG 1 ? ? C8 A DG 1 ? ? N9 A DG 1 ? ? 116.43 113.10 3.33 0.50 N 35 2 N7 A DA 2 ? ? C8 A DA 2 ? ? N9 A DA 2 ? ? 117.25 113.80 3.45 0.50 N 36 2 "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? "C3'" A DC 3 ? ? 109.67 106.00 3.67 0.60 N 37 2 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 100.97 108.00 -7.03 0.70 N 38 2 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 113.56 108.30 5.26 0.30 N 39 2 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 111.55 108.30 3.25 0.30 N 40 2 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.61 122.90 -4.29 0.60 N 41 2 "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? "O4'" A DG 6 ? ? 117.02 109.80 7.22 1.10 N 42 2 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? "C2'" A DG 6 ? ? 100.84 105.90 -5.06 0.80 N 43 2 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 112.98 108.30 4.68 0.30 N 44 2 N7 A DG 6 ? ? C8 A DG 6 ? ? N9 A DG 6 ? ? 116.37 113.10 3.27 0.50 N 45 2 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? "C2'" A DT 7 ? ? 100.15 105.90 -5.75 0.80 N 46 2 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 113.14 108.30 4.84 0.30 N 47 2 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 113.06 108.30 4.76 0.30 N 48 2 N7 B DG 1 ? ? C8 B DG 1 ? ? N9 B DG 1 ? ? 116.45 113.10 3.35 0.50 N 49 2 N7 B DA 2 ? ? C8 B DA 2 ? ? N9 B DA 2 ? ? 117.14 113.80 3.34 0.50 N 50 2 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 101.05 108.00 -6.95 0.70 N 51 2 "O4'" B DA 4 ? ? "C1'" B DA 4 ? ? N9 B DA 4 ? ? 113.49 108.30 5.19 0.30 N 52 2 "O4'" B DT 5 ? ? "C1'" B DT 5 ? ? N1 B DT 5 ? ? 111.66 108.30 3.36 0.30 N 53 2 C6 B DT 5 ? ? C5 B DT 5 ? ? C7 B DT 5 ? ? 118.57 122.90 -4.33 0.60 N 54 2 "C5'" B DG 6 ? ? "C4'" B DG 6 ? ? "O4'" B DG 6 ? ? 117.12 109.80 7.32 1.10 N 55 2 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? "C2'" B DG 6 ? ? 100.96 105.90 -4.94 0.80 N 56 2 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? N9 B DG 6 ? ? 112.95 108.30 4.65 0.30 N 57 2 N7 B DG 6 ? ? C8 B DG 6 ? ? N9 B DG 6 ? ? 116.30 113.10 3.20 0.50 N 58 2 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? "C2'" B DT 7 ? ? 100.05 105.90 -5.85 0.80 N 59 2 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 113.16 108.30 4.86 0.30 N 60 2 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 112.91 108.30 4.61 0.30 N 61 3 N7 A DG 1 ? ? C8 A DG 1 ? ? N9 A DG 1 ? ? 116.31 113.10 3.21 0.50 N 62 3 N7 A DA 2 ? ? C8 A DA 2 ? ? N9 A DA 2 ? ? 117.32 113.80 3.52 0.50 N 63 3 C8 A DA 2 ? ? N9 A DA 2 ? ? C4 A DA 2 ? ? 103.20 105.80 -2.60 0.40 N 64 3 "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? "C3'" A DC 3 ? ? 109.84 106.00 3.84 0.60 N 65 3 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 101.95 108.00 -6.05 0.70 N 66 3 "O4'" A DA 4 ? ? "C4'" A DA 4 ? ? "C3'" A DA 4 ? ? 109.96 106.00 3.96 0.60 N 67 3 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 112.18 108.30 3.88 0.30 N 68 3 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.69 108.30 2.39 0.30 N 69 3 "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? "O4'" A DG 6 ? ? 117.51 109.80 7.71 1.10 N 70 3 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 112.70 108.30 4.40 0.30 N 71 3 N7 A DG 6 ? ? C8 A DG 6 ? ? N9 A DG 6 ? ? 116.73 113.10 3.63 0.50 N 72 3 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? "C2'" A DT 7 ? ? 100.36 105.90 -5.54 0.80 N 73 3 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 114.62 108.30 6.32 0.30 N 74 3 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 112.20 108.30 3.90 0.30 N 75 3 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 122.66 118.90 3.76 0.60 N 76 3 N7 B DG 1 ? ? C8 B DG 1 ? ? N9 B DG 1 ? ? 116.39 113.10 3.29 0.50 N 77 3 N7 B DA 2 ? ? C8 B DA 2 ? ? N9 B DA 2 ? ? 117.40 113.80 3.60 0.50 N 78 3 C8 B DA 2 ? ? N9 B DA 2 ? ? C4 B DA 2 ? ? 103.25 105.80 -2.55 0.40 N 79 3 "O4'" B DC 3 ? ? "C4'" B DC 3 ? ? "C3'" B DC 3 ? ? 109.95 106.00 3.95 0.60 N 80 3 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 102.07 108.00 -5.93 0.70 N 81 3 "O4'" B DA 4 ? ? "C4'" B DA 4 ? ? "C3'" B DA 4 ? ? 109.81 106.00 3.81 0.60 N 82 3 "O4'" B DA 4 ? ? "C1'" B DA 4 ? ? N9 B DA 4 ? ? 112.07 108.30 3.77 0.30 N 83 3 "O4'" B DT 5 ? ? "C1'" B DT 5 ? ? N1 B DT 5 ? ? 110.63 108.30 2.33 0.30 N 84 3 "C5'" B DG 6 ? ? "C4'" B DG 6 ? ? "O4'" B DG 6 ? ? 117.49 109.80 7.69 1.10 N 85 3 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? N9 B DG 6 ? ? 112.87 108.30 4.57 0.30 N 86 3 N7 B DG 6 ? ? C8 B DG 6 ? ? N9 B DG 6 ? ? 116.68 113.10 3.58 0.50 N 87 3 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? "C2'" B DT 7 ? ? 100.55 105.90 -5.35 0.80 N 88 3 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 114.63 108.30 6.33 0.30 N 89 3 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 112.90 108.30 4.60 0.30 N 90 3 N1 B DC 8 ? ? C2 B DC 8 ? ? O2 B DC 8 ? ? 122.66 118.90 3.76 0.60 N 91 4 N7 A DG 1 ? ? C8 A DG 1 ? ? N9 A DG 1 ? ? 116.47 113.10 3.37 0.50 N 92 4 N7 A DA 2 ? ? C8 A DA 2 ? ? N9 A DA 2 ? ? 116.96 113.80 3.16 0.50 N 93 4 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 102.55 108.00 -5.45 0.70 N 94 4 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 113.22 108.30 4.92 0.30 N 95 4 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.66 122.90 -4.24 0.60 N 96 4 N7 A DG 6 ? ? C8 A DG 6 ? ? N9 A DG 6 ? ? 116.39 113.10 3.29 0.50 N 97 4 C8 A DG 6 ? ? N9 A DG 6 ? ? C4 A DG 6 ? ? 103.91 106.40 -2.49 0.40 N 98 4 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 112.26 108.30 3.96 0.30 N 99 4 "C5'" A DC 8 ? ? "C4'" A DC 8 ? ? "O4'" A DC 8 ? ? 116.61 109.80 6.81 1.10 N 100 4 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 112.61 108.30 4.31 0.30 N 101 4 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 122.71 118.90 3.81 0.60 N 102 4 N7 B DG 1 ? ? C8 B DG 1 ? ? N9 B DG 1 ? ? 116.46 113.10 3.36 0.50 N 103 4 N7 B DA 2 ? ? C8 B DA 2 ? ? N9 B DA 2 ? ? 117.12 113.80 3.32 0.50 N 104 4 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 102.57 108.00 -5.43 0.70 N 105 4 "O4'" B DA 4 ? ? "C1'" B DA 4 ? ? N9 B DA 4 ? ? 113.25 108.30 4.95 0.30 N 106 4 C6 B DT 5 ? ? C5 B DT 5 ? ? C7 B DT 5 ? ? 118.94 122.90 -3.96 0.60 N 107 4 N7 B DG 6 ? ? C8 B DG 6 ? ? N9 B DG 6 ? ? 116.35 113.10 3.25 0.50 N 108 4 C8 B DG 6 ? ? N9 B DG 6 ? ? C4 B DG 6 ? ? 103.96 106.40 -2.44 0.40 N 109 4 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 112.32 108.30 4.02 0.30 N 110 4 "C5'" B DC 8 ? ? "C4'" B DC 8 ? ? "O4'" B DC 8 ? ? 116.58 109.80 6.78 1.10 N 111 4 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 112.66 108.30 4.36 0.30 N 112 4 N1 B DC 8 ? ? C2 B DC 8 ? ? O2 B DC 8 ? ? 122.67 118.90 3.77 0.60 N # _pdbx_nmr_ensemble.entry_id 202D _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_details.entry_id 202D _pdbx_nmr_details.text 'MENOGARIL WAS PROVIDED BY UPJOHN CO., KALAMAZOO, MICHIGAN.' # _pdbx_nmr_refine.entry_id 202D _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 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 30, 60, 100, 150 AND 200 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 0.039 0.038 0.038 0.036 BOND (ANG) 0.012 0.012 0.012 0.011 ANGLES (DEG) 3.833 3.818 3.776 3.684 IMPROPERS (DEG) 0.251 0.250 0.286 0.219 ; _pdbx_nmr_refine.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 MNG C1 C Y N 144 MNG C2 C Y N 145 MNG C3 C Y N 146 MNG C4 C Y N 147 MNG C5 C N N 148 MNG C6 C Y N 149 MNG C7 C N R 150 MNG C8 C N N 151 MNG C9 C N R 152 MNG C10 C N N 153 MNG C11 C Y N 154 MNG C12 C N N 155 MNG C16 C Y N 156 MNG C17 C Y N 157 MNG C18 C Y N 158 MNG C19 C Y N 159 MNG C20 C Y N 160 MNG C21 C Y N 161 MNG "C1'" C N S 162 MNG "C2'" C N S 163 MNG "C3'" C N R 164 MNG "C4'" C N R 165 MNG "C5'" C N R 166 MNG C5M C N N 167 MNG C1M C N N 168 MNG C2M C N N 169 MNG C7M C N N 170 MNG C9M C N N 171 MNG O1 O N N 172 MNG O4 O N N 173 MNG O5 O N N 174 MNG O6 O N N 175 MNG O7 O N N 176 MNG O9 O N N 177 MNG O12 O N N 178 MNG "O1'" O N N 179 MNG "O2'" O N N 180 MNG "O4'" O N N 181 MNG N1 N N N 182 MNG H3 H N N 183 MNG H7 H N N 184 MNG H81 H N N 185 MNG H82 H N N 186 MNG H101 H N N 187 MNG H102 H N N 188 MNG H11 H N N 189 MNG "H1'" H N N 190 MNG "H2'" H N N 191 MNG "H3'" H N N 192 MNG "H4'" H N N 193 MNG H5M1 H N N 194 MNG H5M2 H N N 195 MNG H5M3 H N N 196 MNG H1M1 H N N 197 MNG H1M2 H N N 198 MNG H1M3 H N N 199 MNG H2M1 H N N 200 MNG H2M2 H N N 201 MNG H2M3 H N N 202 MNG H7M1 H N N 203 MNG H7M2 H N N 204 MNG H7M3 H N N 205 MNG H9M1 H N N 206 MNG H9M2 H N N 207 MNG H9M3 H N N 208 MNG HO4 H N N 209 MNG HO6 H N N 210 MNG HO9 H N N 211 MNG "HO2'" H N N 212 MNG "HO4'" H N N 213 # 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 MNG C1 C2 doub Y N 150 MNG C1 C16 sing Y N 151 MNG C1 O1 sing N N 152 MNG C2 C3 sing Y N 153 MNG C2 "C5'" sing N N 154 MNG C3 C4 doub Y N 155 MNG C3 H3 sing N N 156 MNG C4 C17 sing Y N 157 MNG C4 O4 sing N N 158 MNG C5 C17 sing N N 159 MNG C5 C18 sing N N 160 MNG C5 O5 doub N N 161 MNG C6 C18 doub Y N 162 MNG C6 C19 sing Y N 163 MNG C6 O6 sing N N 164 MNG C7 C8 sing N N 165 MNG C7 C19 sing N N 166 MNG C7 O7 sing N N 167 MNG C7 H7 sing N N 168 MNG C8 C9 sing N N 169 MNG C8 H81 sing N N 170 MNG C8 H82 sing N N 171 MNG C9 C10 sing N N 172 MNG C9 C9M sing N N 173 MNG C9 O9 sing N N 174 MNG C10 C20 sing N N 175 MNG C10 H101 sing N N 176 MNG C10 H102 sing N N 177 MNG C11 C20 sing Y N 178 MNG C11 C21 doub Y N 179 MNG C11 H11 sing N N 180 MNG C12 C16 sing N N 181 MNG C12 C21 sing N N 182 MNG C12 O12 doub N N 183 MNG C16 C17 doub Y N 184 MNG C18 C21 sing Y N 185 MNG C19 C20 doub Y N 186 MNG "C1'" "C2'" sing N N 187 MNG "C1'" O1 sing N N 188 MNG "C1'" "O1'" sing N N 189 MNG "C1'" "H1'" sing N N 190 MNG "C2'" "C3'" sing N N 191 MNG "C2'" "O2'" sing N N 192 MNG "C2'" "H2'" sing N N 193 MNG "C3'" "C4'" sing N N 194 MNG "C3'" N1 sing N N 195 MNG "C3'" "H3'" sing N N 196 MNG "C4'" "C5'" sing N N 197 MNG "C4'" "O4'" sing N N 198 MNG "C4'" "H4'" sing N N 199 MNG "C5'" C5M sing N N 200 MNG "C5'" "O1'" sing N N 201 MNG C5M H5M1 sing N N 202 MNG C5M H5M2 sing N N 203 MNG C5M H5M3 sing N N 204 MNG C1M N1 sing N N 205 MNG C1M H1M1 sing N N 206 MNG C1M H1M2 sing N N 207 MNG C1M H1M3 sing N N 208 MNG C2M N1 sing N N 209 MNG C2M H2M1 sing N N 210 MNG C2M H2M2 sing N N 211 MNG C2M H2M3 sing N N 212 MNG C7M O7 sing N N 213 MNG C7M H7M1 sing N N 214 MNG C7M H7M2 sing N N 215 MNG C7M H7M3 sing N N 216 MNG C9M H9M1 sing N N 217 MNG C9M H9M2 sing N N 218 MNG C9M H9M3 sing N N 219 MNG O4 HO4 sing N N 220 MNG O6 HO6 sing N N 221 MNG O9 HO9 sing N N 222 MNG "O2'" "HO2'" sing N N 223 MNG "O4'" "HO4'" sing N N 224 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 202D 'double helix' 202D '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 DG 1 1_555 B DC 8 1_555 -0.591 -0.277 -0.480 -13.858 -4.520 -1.390 1 A_DG1:DC8_B A 1 ? B 8 ? 19 1 1 A DA 2 1_555 B DT 7 1_555 0.052 -0.224 0.076 -1.375 -0.127 -4.846 2 A_DA2:DT7_B A 2 ? B 7 ? 20 1 1 A DC 3 1_555 B DG 6 1_555 0.563 -0.194 -0.254 21.007 2.147 5.771 3 A_DC3:DG6_B A 3 ? B 6 ? 19 1 1 A DA 4 1_555 B DT 5 1_555 0.413 -0.134 -0.326 -11.933 12.748 -1.967 4 A_DA4:DT5_B A 4 ? B 5 ? 20 1 1 A DT 5 1_555 B DA 4 1_555 -0.483 -0.129 -0.295 12.041 11.920 -2.787 5 A_DT5:DA4_B A 5 ? B 4 ? 20 1 1 A DG 6 1_555 B DC 3 1_555 -0.514 -0.191 -0.235 -20.959 0.918 5.381 6 A_DG6:DC3_B A 6 ? B 3 ? 19 1 1 A DT 7 1_555 B DA 2 1_555 0.000 -0.241 0.038 0.632 -1.215 -4.687 7 A_DT7:DA2_B A 7 ? B 2 ? 20 1 1 A DC 8 1_555 B DG 1 1_555 0.612 -0.258 -0.485 11.890 -3.519 -1.122 8 A_DC8:DG1_B A 8 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 B DC 8 1_555 A DA 2 1_555 B DT 7 1_555 -1.288 0.206 2.928 -6.950 -4.683 42.968 0.690 1.116 3.052 -6.322 9.381 43.740 1 AA_DG1DA2:DT7DC8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A DA 2 1_555 B DT 7 1_555 A DC 3 1_555 B DG 6 1_555 1.342 0.078 2.631 0.510 -2.031 29.405 0.504 -2.549 2.642 -3.995 -1.002 29.478 2 AA_DA2DC3:DG6DT7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A DC 3 1_555 B DG 6 1_555 A DA 4 1_555 B DT 5 1_555 -0.461 0.563 6.734 -2.941 -3.531 30.152 2.516 -0.328 6.640 -6.738 5.612 30.492 3 AA_DC3DA4:DT5DG6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A DA 4 1_555 B DT 5 1_555 A DT 5 1_555 B DA 4 1_555 -0.061 -0.187 3.246 0.015 15.483 15.911 -6.209 0.164 2.207 44.486 -0.042 22.166 4 AA_DA4DT5:DA4DT5_BB A 4 ? B 5 ? A 5 ? B 4 ? 1 A DT 5 1_555 B DA 4 1_555 A DG 6 1_555 B DC 3 1_555 0.466 0.574 6.692 3.084 -3.050 30.951 2.248 0.331 6.620 -5.680 -5.744 31.246 5 AA_DT5DG6:DC3DA4_BB A 5 ? B 4 ? A 6 ? B 3 ? 1 A DG 6 1_555 B DC 3 1_555 A DT 7 1_555 B DA 2 1_555 -1.319 0.059 2.633 -0.462 -1.337 29.593 0.343 2.500 2.648 -2.615 0.903 29.626 6 AA_DG6DT7:DA2DC3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A DT 7 1_555 B DA 2 1_555 A DC 8 1_555 B DG 1 1_555 1.273 0.201 2.966 6.696 -3.252 42.876 0.565 -1.114 3.099 -4.408 -9.078 43.487 7 AA_DT7DC8:DG1DA2_BB A 7 ? B 2 ? A 8 ? B 1 ? # _atom_sites.entry_id 202D _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_ #