data_9WPJ # _entry.id 9WPJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.416 _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 9WPJ pdb_00009wpj 10.2210/pdb9wpj/pdb WWPDB D_1300063073 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-09-09 _pdbx_audit_revision_history.part_number ? # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9WPJ _pdbx_database_status.recvd_initial_deposition_date 2025-09-09 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email mhho@dragon.nchu.edu.tw _pdbx_contact_author.name_first 'Ming Hon' _pdbx_contact_author.name_last Hou _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-4170-1527 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Tsai, C.J.' 1 0009-0005-2321-7514 'Huang, Y.Z.' 2 0009-0009-2286-839X 'Hou, M.H.' 3 0000-0003-4170-1527 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Crystal structure of Actinomycin D with d(AGGGCGCGT/AGGGCGCGT)' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Tsai, C.J.' 1 0009-0009-2286-839X primary 'Huang, Y.Z.' 2 0009-0009-2286-839X primary 'Hou, M.H.' 3 0000-0003-4170-1527 # 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 'Actinomycin D' 1291.446 4 ? ? ? ? 2 polymer syn ;DNA (5'-D(*AP*GP*GP*CP*GP*CP*GP*T)-3') ; 2467.629 2 ? ? ? ? 3 non-polymer syn 'DI(HYDROXYETHYL)ETHER' 106.120 1 ? ? ? ? 4 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 5 water nat water 18.015 218 ? ? ? ? # 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 'polypeptide(L)' no yes 'T(DVA)P(SAR)(MVA)(PXZ)T(DVA)P(SAR)(MVA)' TVPGVXTVPGV C,D,E,F ? 2 polydeoxyribonucleotide no no '(DA)(DG)(DG)(DC)(DG)(DC)(DG)(DT)' AGGCGCGT A,B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'DI(HYDROXYETHYL)ETHER' PEG 4 GLYCEROL GOL 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 THR n 1 2 DVA n 1 3 PRO n 1 4 SAR n 1 5 MVA n 1 6 PXZ n 1 7 THR n 1 8 DVA n 1 9 PRO n 1 10 SAR n 1 11 MVA n 2 1 DA n 2 2 DG n 2 3 DG n 2 4 DC n 2 5 DG n 2 6 DC n 2 7 DG n 2 8 DT 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 1 11 'Streptomyces antibioticus' ? 1890 ? 2 1 sample 1 8 'Homo sapiens' ? 9606 ? # 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 DVA 'D-peptide linking' . D-VALINE ? 'C5 H11 N O2' 117.146 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HOH non-polymer . WATER ? 'H2 O' 18.015 MVA 'L-peptide linking' n N-METHYLVALINE ? 'C6 H13 N O2' 131.173 PEG non-polymer . 'DI(HYDROXYETHYL)ETHER' ? 'C4 H10 O3' 106.120 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 PXZ non-polymer . 2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE PHENOXAZINE 'C16 H12 N2 O6' 328.276 SAR 'peptide linking' n SARCOSINE ? 'C3 H7 N O2' 89.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 # 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 THR 1 1 1 THR THR C . n A 1 2 DVA 2 2 2 DVA DVA C . n A 1 3 PRO 3 3 3 PRO PRO C . n A 1 4 SAR 4 4 4 SAR SAR C . n A 1 5 MVA 5 5 5 MVA MVA C . n A 1 6 PXZ 6 6 6 PXZ PXZ C . n A 1 7 THR 7 7 7 THR THR C . n A 1 8 DVA 8 8 8 DVA DVA C . n A 1 9 PRO 9 9 9 PRO PRO C . n A 1 10 SAR 10 10 10 SAR SAR C . n A 1 11 MVA 11 11 11 MVA MVA C . n B 1 1 THR 1 1 1 THR THR D . n B 1 2 DVA 2 2 2 DVA DVA D . n B 1 3 PRO 3 3 3 PRO PRO D . n B 1 4 SAR 4 4 4 SAR SAR D . n B 1 5 MVA 5 5 5 MVA MVA D . n B 1 6 PXZ 6 6 6 PXZ PXZ D . n B 1 7 THR 7 7 7 THR THR D . n B 1 8 DVA 8 8 8 DVA DVA D . n B 1 9 PRO 9 9 9 PRO PRO D . n B 1 10 SAR 10 10 10 SAR SAR D . n B 1 11 MVA 11 11 11 MVA MVA D . n C 2 1 DA 1 1 1 DA DA A . n C 2 2 DG 2 2 2 DG DG A . n C 2 3 DG 3 3 3 DG DG A . n C 2 4 DC 4 4 4 DC DC A . n C 2 5 DG 5 5 5 DG DG A . n C 2 6 DC 6 6 6 DC DC A . n C 2 7 DG 7 7 7 DG DG A . n C 2 8 DT 8 8 8 DT DT A . n D 1 1 THR 1 1 1 THR THR E . n D 1 2 DVA 2 2 2 DVA DVA E . n D 1 3 PRO 3 3 3 PRO PRO E . n D 1 4 SAR 4 4 4 SAR SAR E . n D 1 5 MVA 5 5 5 MVA MVA E . n D 1 6 PXZ 6 6 6 PXZ PXZ E . n D 1 7 THR 7 7 7 THR THR E . n D 1 8 DVA 8 8 8 DVA DVA E . n D 1 9 PRO 9 9 9 PRO PRO E . n D 1 10 SAR 10 10 10 SAR SAR E . n D 1 11 MVA 11 11 11 MVA MVA E . n E 1 1 THR 1 1 1 THR THR F . n E 1 2 DVA 2 2 2 DVA DVA F . n E 1 3 PRO 3 3 3 PRO PRO F . n E 1 4 SAR 4 4 4 SAR SAR F . n E 1 5 MVA 5 5 5 MVA MVA F . n E 1 6 PXZ 6 6 6 PXZ PXZ F . n E 1 7 THR 7 7 7 THR THR F . n E 1 8 DVA 8 8 8 DVA DVA F . n E 1 9 PRO 9 9 9 PRO PRO F . n E 1 10 SAR 10 10 10 SAR SAR F . n E 1 11 MVA 11 11 11 MVA MVA F . n F 2 1 DA 1 1 1 DA DA B . n F 2 2 DG 2 2 2 DG DG B . n F 2 3 DG 3 3 3 DG DG B . n F 2 4 DC 4 4 4 DC DC B . n F 2 5 DG 5 5 5 DG DG B . n F 2 6 DC 6 6 6 DC DC B . n F 2 7 DG 7 7 7 DG DG B . n F 2 8 DT 8 8 8 DT DT B . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id PXZ _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id PXZ _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # 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 G 3 PEG 1 101 1 PEG PEG D . H 4 GOL 1 101 2 GOL GOL A . I 5 HOH 1 101 13 HOH HOH C . I 5 HOH 2 102 20 HOH HOH C . I 5 HOH 3 103 43 HOH HOH C . I 5 HOH 4 104 30 HOH HOH C . I 5 HOH 5 105 60 HOH HOH C . I 5 HOH 6 106 156 HOH HOH C . I 5 HOH 7 107 84 HOH HOH C . I 5 HOH 8 108 62 HOH HOH C . I 5 HOH 9 109 109 HOH HOH C . I 5 HOH 10 110 102 HOH HOH C . I 5 HOH 11 111 81 HOH HOH C . I 5 HOH 12 112 40 HOH HOH C . J 5 HOH 1 201 45 HOH HOH D . J 5 HOH 2 202 41 HOH HOH D . J 5 HOH 3 203 42 HOH HOH D . J 5 HOH 4 204 80 HOH HOH D . J 5 HOH 5 205 111 HOH HOH D . J 5 HOH 6 206 110 HOH HOH D . J 5 HOH 7 207 87 HOH HOH D . J 5 HOH 8 208 222 HOH HOH D . J 5 HOH 9 209 89 HOH HOH D . J 5 HOH 10 210 52 HOH HOH D . J 5 HOH 11 211 209 HOH HOH D . J 5 HOH 12 212 101 HOH HOH D . J 5 HOH 13 213 79 HOH HOH D . J 5 HOH 14 214 88 HOH HOH D . J 5 HOH 15 215 169 HOH HOH D . J 5 HOH 16 216 174 HOH HOH D . J 5 HOH 17 217 140 HOH HOH D . J 5 HOH 18 218 145 HOH HOH D . J 5 HOH 19 219 112 HOH HOH D . J 5 HOH 20 220 141 HOH HOH D . K 5 HOH 1 201 57 HOH HOH A . K 5 HOH 2 202 61 HOH HOH A . K 5 HOH 3 203 98 HOH HOH A . K 5 HOH 4 204 4 HOH HOH A . K 5 HOH 5 205 36 HOH HOH A . K 5 HOH 6 206 69 HOH HOH A . K 5 HOH 7 207 11 HOH HOH A . K 5 HOH 8 208 23 HOH HOH A . K 5 HOH 9 209 75 HOH HOH A . K 5 HOH 10 210 15 HOH HOH A . K 5 HOH 11 211 9 HOH HOH A . K 5 HOH 12 212 12 HOH HOH A . K 5 HOH 13 213 99 HOH HOH A . K 5 HOH 14 214 215 HOH HOH A . K 5 HOH 15 215 33 HOH HOH A . K 5 HOH 16 216 22 HOH HOH A . K 5 HOH 17 217 224 HOH HOH A . K 5 HOH 18 218 38 HOH HOH A . K 5 HOH 19 219 49 HOH HOH A . K 5 HOH 20 220 207 HOH HOH A . K 5 HOH 21 221 151 HOH HOH A . K 5 HOH 22 222 123 HOH HOH A . K 5 HOH 23 223 63 HOH HOH A . K 5 HOH 24 224 39 HOH HOH A . K 5 HOH 25 225 29 HOH HOH A . K 5 HOH 26 226 70 HOH HOH A . K 5 HOH 27 227 46 HOH HOH A . K 5 HOH 28 228 44 HOH HOH A . K 5 HOH 29 229 97 HOH HOH A . K 5 HOH 30 230 86 HOH HOH A . K 5 HOH 31 231 95 HOH HOH A . K 5 HOH 32 232 122 HOH HOH A . K 5 HOH 33 233 166 HOH HOH A . K 5 HOH 34 234 205 HOH HOH A . K 5 HOH 35 235 208 HOH HOH A . K 5 HOH 36 236 171 HOH HOH A . K 5 HOH 37 237 58 HOH HOH A . K 5 HOH 38 238 66 HOH HOH A . K 5 HOH 39 239 26 HOH HOH A . K 5 HOH 40 240 94 HOH HOH A . K 5 HOH 41 241 117 HOH HOH A . K 5 HOH 42 242 187 HOH HOH A . K 5 HOH 43 243 202 HOH HOH A . K 5 HOH 44 244 185 HOH HOH A . K 5 HOH 45 245 168 HOH HOH A . K 5 HOH 46 246 186 HOH HOH A . K 5 HOH 47 247 190 HOH HOH A . K 5 HOH 48 248 35 HOH HOH A . K 5 HOH 49 249 78 HOH HOH A . K 5 HOH 50 250 201 HOH HOH A . K 5 HOH 51 251 118 HOH HOH A . K 5 HOH 52 252 223 HOH HOH A . K 5 HOH 53 253 96 HOH HOH A . K 5 HOH 54 254 221 HOH HOH A . K 5 HOH 55 255 100 HOH HOH A . K 5 HOH 56 256 194 HOH HOH A . K 5 HOH 57 257 124 HOH HOH A . K 5 HOH 58 258 146 HOH HOH A . K 5 HOH 59 259 82 HOH HOH A . K 5 HOH 60 260 180 HOH HOH A . K 5 HOH 61 261 93 HOH HOH A . K 5 HOH 62 262 155 HOH HOH A . K 5 HOH 63 263 219 HOH HOH A . K 5 HOH 64 264 198 HOH HOH A . K 5 HOH 65 265 204 HOH HOH A . K 5 HOH 66 266 147 HOH HOH A . K 5 HOH 67 267 137 HOH HOH A . K 5 HOH 68 268 149 HOH HOH A . K 5 HOH 69 269 148 HOH HOH A . K 5 HOH 70 270 138 HOH HOH A . K 5 HOH 71 271 220 HOH HOH A . K 5 HOH 72 272 152 HOH HOH A . K 5 HOH 73 273 139 HOH HOH A . K 5 HOH 74 274 193 HOH HOH A . L 5 HOH 1 101 59 HOH HOH E . L 5 HOH 2 102 50 HOH HOH E . L 5 HOH 3 103 77 HOH HOH E . L 5 HOH 4 104 32 HOH HOH E . L 5 HOH 5 105 27 HOH HOH E . L 5 HOH 6 106 10 HOH HOH E . L 5 HOH 7 107 161 HOH HOH E . L 5 HOH 8 108 127 HOH HOH E . L 5 HOH 9 109 48 HOH HOH E . L 5 HOH 10 110 150 HOH HOH E . L 5 HOH 11 111 55 HOH HOH E . L 5 HOH 12 112 7 HOH HOH E . L 5 HOH 13 113 225 HOH HOH E . L 5 HOH 14 114 135 HOH HOH E . L 5 HOH 15 115 103 HOH HOH E . L 5 HOH 16 116 203 HOH HOH E . M 5 HOH 1 101 67 HOH HOH F . M 5 HOH 2 102 68 HOH HOH F . M 5 HOH 3 103 64 HOH HOH F . M 5 HOH 4 104 3 HOH HOH F . M 5 HOH 5 105 19 HOH HOH F . M 5 HOH 6 106 119 HOH HOH F . M 5 HOH 7 107 125 HOH HOH F . M 5 HOH 8 108 129 HOH HOH F . M 5 HOH 9 109 130 HOH HOH F . M 5 HOH 10 110 16 HOH HOH F . M 5 HOH 11 111 54 HOH HOH F . M 5 HOH 12 112 53 HOH HOH F . M 5 HOH 13 113 51 HOH HOH F . M 5 HOH 14 114 206 HOH HOH F . M 5 HOH 15 115 173 HOH HOH F . M 5 HOH 16 116 226 HOH HOH F . M 5 HOH 17 117 170 HOH HOH F . N 5 HOH 1 101 8 HOH HOH B . N 5 HOH 2 102 14 HOH HOH B . N 5 HOH 3 103 25 HOH HOH B . N 5 HOH 4 104 56 HOH HOH B . N 5 HOH 5 105 71 HOH HOH B . N 5 HOH 6 106 6 HOH HOH B . N 5 HOH 7 107 1 HOH HOH B . N 5 HOH 8 108 177 HOH HOH B . N 5 HOH 9 109 120 HOH HOH B . N 5 HOH 10 110 128 HOH HOH B . N 5 HOH 11 111 230 HOH HOH B . N 5 HOH 12 112 160 HOH HOH B . N 5 HOH 13 113 34 HOH HOH B . N 5 HOH 14 114 2 HOH HOH B . N 5 HOH 15 115 126 HOH HOH B . N 5 HOH 16 116 18 HOH HOH B . N 5 HOH 17 117 211 HOH HOH B . N 5 HOH 18 118 21 HOH HOH B . N 5 HOH 19 119 212 HOH HOH B . N 5 HOH 20 120 162 HOH HOH B . N 5 HOH 21 121 213 HOH HOH B . N 5 HOH 22 122 47 HOH HOH B . N 5 HOH 23 123 90 HOH HOH B . N 5 HOH 24 124 37 HOH HOH B . N 5 HOH 25 125 5 HOH HOH B . N 5 HOH 26 126 85 HOH HOH B . N 5 HOH 27 127 31 HOH HOH B . N 5 HOH 28 128 172 HOH HOH B . N 5 HOH 29 129 17 HOH HOH B . N 5 HOH 30 130 76 HOH HOH B . N 5 HOH 31 131 210 HOH HOH B . N 5 HOH 32 132 191 HOH HOH B . N 5 HOH 33 133 192 HOH HOH B . N 5 HOH 34 134 217 HOH HOH B . N 5 HOH 35 135 65 HOH HOH B . N 5 HOH 36 136 121 HOH HOH B . N 5 HOH 37 137 136 HOH HOH B . N 5 HOH 38 138 176 HOH HOH B . N 5 HOH 39 139 104 HOH HOH B . N 5 HOH 40 140 108 HOH HOH B . N 5 HOH 41 141 134 HOH HOH B . N 5 HOH 42 142 200 HOH HOH B . N 5 HOH 43 143 216 HOH HOH B . N 5 HOH 44 144 214 HOH HOH B . N 5 HOH 45 145 199 HOH HOH B . N 5 HOH 46 146 72 HOH HOH B . N 5 HOH 47 147 92 HOH HOH B . N 5 HOH 48 148 165 HOH HOH B . N 5 HOH 49 149 175 HOH HOH B . N 5 HOH 50 150 91 HOH HOH B . N 5 HOH 51 151 114 HOH HOH B . N 5 HOH 52 152 24 HOH HOH B . N 5 HOH 53 153 105 HOH HOH B . N 5 HOH 54 154 83 HOH HOH B . N 5 HOH 55 155 28 HOH HOH B . N 5 HOH 56 156 132 HOH HOH B . N 5 HOH 57 157 159 HOH HOH B . N 5 HOH 58 158 218 HOH HOH B . N 5 HOH 59 159 131 HOH HOH B . N 5 HOH 60 160 195 HOH HOH B . N 5 HOH 61 161 107 HOH HOH B . N 5 HOH 62 162 229 HOH HOH B . N 5 HOH 63 163 106 HOH HOH B . N 5 HOH 64 164 163 HOH HOH B . N 5 HOH 65 165 197 HOH HOH B . N 5 HOH 66 166 167 HOH HOH B . N 5 HOH 67 167 189 HOH HOH B . N 5 HOH 68 168 154 HOH HOH B . N 5 HOH 69 169 74 HOH HOH B . N 5 HOH 70 170 144 HOH HOH B . N 5 HOH 71 171 133 HOH HOH B . N 5 HOH 72 172 179 HOH HOH B . N 5 HOH 73 173 113 HOH HOH B . N 5 HOH 74 174 143 HOH HOH B . N 5 HOH 75 175 142 HOH HOH B . N 5 HOH 76 176 153 HOH HOH B . N 5 HOH 77 177 116 HOH HOH B . N 5 HOH 78 178 115 HOH HOH B . N 5 HOH 79 179 196 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A DA 1 ? "O5'" ? C DA 1 "O5'" 2 1 Y 1 B DA 1 ? "O5'" ? F DA 1 "O5'" # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_reference_DOI _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(2.0_5885: ???)' ? 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . ? 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? . ? 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . ? 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . ? 5 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 121.86 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 9WPJ _cell.details ? _cell.formula_units_Z ? _cell.length_a 78.631 _cell.length_a_esd ? _cell.length_b 44.892 _cell.length_b_esd ? _cell.length_c 41.695 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 16 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9WPJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9WPJ _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 3.07 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 59.96 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'Glycerol, PEG500 MME, Bis-Tris buffer, Ammonium sulfate' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 298 # _diffrn.ambient_environment ? _diffrn.ambient_temp 298 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2022-10-05 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'NSRRC BEAMLINE TPS 07A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.0 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 'TPS 07A' _diffrn_source.pdbx_synchrotron_site NSRRC # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 9WPJ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.61 _reflns.d_resolution_low 30.00 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 14667 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 90.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.3 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 10.3 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.059 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.072 _reflns.pdbx_Rpim_I_all 0.039 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 48140 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.989 _reflns.pdbx_CC_star 0.997 _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.060 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 1.61 1.67 ? ? ? ? ? ? 1527 ? ? ? ? ? ? ? ? ? ? ? 3.5 1.055 ? ? 0.449 0.234 ? 1 1 0.901 0.973 ? 95.7 ? 0.381 ? ? ? ? ? ? ? ? ? 1.67 1.73 ? ? ? ? ? ? 1519 ? ? ? ? ? ? ? ? ? ? ? 3.5 1.077 ? ? 0.314 0.163 ? 2 1 0.947 0.986 ? 95.4 ? 0.266 ? ? ? ? ? ? ? ? ? 1.73 1.81 ? ? ? ? ? ? 1561 ? ? ? ? ? ? ? ? ? ? ? 3.5 1.079 ? ? 0.245 0.128 ? 3 1 0.955 0.988 ? 95.6 ? 0.208 ? ? ? ? ? ? ? ? ? 1.81 1.91 ? ? ? ? ? ? 1472 ? ? ? ? ? ? ? ? ? ? ? 3.2 1.062 ? ? 0.185 0.100 ? 4 1 0.969 0.992 ? 92.6 ? 0.154 ? ? ? ? ? ? ? ? ? 1.91 2.03 ? ? ? ? ? ? 1465 ? ? ? ? ? ? ? ? ? ? ? 3.3 1.082 ? ? 0.139 0.075 ? 5 1 0.984 0.996 ? 92.7 ? 0.117 ? ? ? ? ? ? ? ? ? 2.03 2.18 ? ? ? ? ? ? 1555 ? ? ? ? ? ? ? ? ? ? ? 3.4 1.041 ? ? 0.121 0.065 ? 6 1 0.985 0.996 ? 94.8 ? 0.102 ? ? ? ? ? ? ? ? ? 2.18 2.40 ? ? ? ? ? ? 1462 ? ? ? ? ? ? ? ? ? ? ? 3.3 1.056 ? ? 0.099 0.052 ? 7 1 0.990 0.997 ? 91.8 ? 0.083 ? ? ? ? ? ? ? ? ? 2.40 2.75 ? ? ? ? ? ? 1428 ? ? ? ? ? ? ? ? ? ? ? 3.1 1.017 ? ? 0.077 0.041 ? 8 1 0.995 0.999 ? 88.8 ? 0.065 ? ? ? ? ? ? ? ? ? 2.75 3.47 ? ? ? ? ? ? 1373 ? ? ? ? ? ? ? ? ? ? ? 3.0 1.073 ? ? 0.063 0.035 ? 9 1 0.995 0.999 ? 83.7 ? 0.051 ? ? ? ? ? ? ? ? ? 3.47 30.00 ? ? ? ? ? ? 1305 ? ? ? ? ? ? ? ? ? ? ? 2.8 1.044 ? ? 0.052 0.028 ? 10 1 0.994 0.999 ? 78.4 ? 0.043 ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9WPJ _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.61 _refine.ls_d_res_low 22.52 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 14617 _refine.ls_number_reflns_R_free 1472 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 90.40 _refine.ls_percent_reflns_R_free 10.07 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2242 _refine.ls_R_factor_R_free 0.2701 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2190 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.36 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 31.09 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.24 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.61 _refine_hist.d_res_low 22.52 _refine_hist.number_atoms_solvent 218 _refine_hist.number_atoms_total 917 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 360 _refine_hist.pdbx_number_atoms_nucleic_acid 326 _refine_hist.pdbx_number_atoms_ligand 13 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_Zscore _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.007 ? 761 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 1.245 ? 1102 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 26.440 ? 256 ? f_dihedral_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.043 ? 110 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.009 ? 76 ? f_plane_restr ? ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.correlation_coeff_Fo_to_Fc _refine_ls_shell.correlation_coeff_Fo_to_Fc_free _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.61 1.66 . . 134 1216 92.00 . . . . 0.2773 . . . . . . . . . . . . . . . 0.3739 'X-RAY DIFFRACTION' 1.66 1.72 . . 129 1236 95.00 . . . . 0.2676 . . . . . . . . . . . . . . . 0.2817 'X-RAY DIFFRACTION' 1.72 1.79 . . 140 1258 96.00 . . . . 0.2523 . . . . . . . . . . . . . . . 0.2958 'X-RAY DIFFRACTION' 1.79 1.87 . . 149 1226 93.00 . . . . 0.2437 . . . . . . . . . . . . . . . 0.3252 'X-RAY DIFFRACTION' 1.87 1.97 . . 136 1195 91.00 . . . . 0.2465 . . . . . . . . . . . . . . . 0.3110 'X-RAY DIFFRACTION' 1.97 2.09 . . 124 1239 95.00 . . . . 0.2420 . . . . . . . . . . . . . . . 0.3147 'X-RAY DIFFRACTION' 2.09 2.25 . . 154 1236 93.00 . . . . 0.2443 . . . . . . . . . . . . . . . 0.3054 'X-RAY DIFFRACTION' 2.25 2.48 . . 135 1206 91.00 . . . . 0.2391 . . . . . . . . . . . . . . . 0.3390 'X-RAY DIFFRACTION' 2.48 2.84 . . 134 1158 87.00 . . . . 0.2502 . . . . . . . . . . . . . . . 0.2852 'X-RAY DIFFRACTION' 2.84 3.57 . . 123 1097 83.00 . . . . 0.2017 . . . . . . . . . . . . . . . 0.2528 'X-RAY DIFFRACTION' 3.57 22.52 . . 114 1078 78.00 . . . . 0.1748 . . . . . . . . . . . . . . . 0.2009 # _struct.entry_id 9WPJ _struct.title 'Crystal structure of Actinomycin D with d(AGGCGCGT/AGGCGCGT)' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9WPJ _struct_keywords.text 'Bubble structure, Structure genomics, DNA, DNA-ANTIBIOTIC complex' _struct_keywords.pdbx_keywords DNA/ANTIBIOTIC # 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 1 ? E N N 1 ? F N N 2 ? G N N 3 ? H N N 4 ? I N N 5 ? J N N 5 ? K N N 5 ? L N N 5 ? M N N 5 ? N N N 5 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 NOR 9WPJ NOR00228 ? 1 ? 1 2 PDB 9WPJ 9WPJ ? 2 ? 1 # 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 9WPJ C 1 ? 11 ? 9WPJ 1 ? 11 ? 1 11 2 1 9WPJ D 1 ? 11 ? 9WPJ 1 ? 11 ? 1 11 3 2 9WPJ A 1 ? 8 ? 9WPJ 1 ? 8 ? 1 8 4 1 9WPJ E 1 ? 11 ? 9WPJ 1 ? 11 ? 1 11 5 1 9WPJ F 1 ? 11 ? 9WPJ 1 ? 11 ? 1 11 6 2 9WPJ B 1 ? 8 ? 9WPJ 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 hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _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_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A THR 1 C ? ? ? 1_555 A DVA 2 N ? ? C THR 1 C DVA 2 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale2 covale one ? A THR 1 OG1 ? ? ? 1_555 A MVA 5 C ? ? C THR 1 C MVA 5 1_555 ? ? ? ? ? ? ? 1.371 ? ? covale3 covale both ? A THR 1 N ? ? ? 1_555 A PXZ 6 C0 ? ? C THR 1 C PXZ 6 1_555 ? ? ? ? ? ? ? 1.423 ? ? covale4 covale both ? A DVA 2 C ? ? ? 1_555 A PRO 3 N ? ? C DVA 2 C PRO 3 1_555 ? ? ? ? ? ? ? 1.347 ? ? covale5 covale both ? A PRO 3 C ? ? ? 1_555 A SAR 4 N ? ? C PRO 3 C SAR 4 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale6 covale both ? A SAR 4 C ? ? ? 1_555 A MVA 5 N ? ? C SAR 4 C MVA 5 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale7 covale both ? A PXZ 6 "C0'" ? ? ? 1_555 A THR 7 N ? ? C PXZ 6 C THR 7 1_555 ? ? ? ? ? ? ? 1.425 ? ? covale8 covale both ? A THR 7 C ? ? ? 1_555 A DVA 8 N ? ? C THR 7 C DVA 8 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale9 covale one ? A THR 7 OG1 ? ? ? 1_555 A MVA 11 C ? ? C THR 7 C MVA 11 1_555 ? ? ? ? ? ? ? 1.372 ? ? covale10 covale both ? A DVA 8 C ? ? ? 1_555 A PRO 9 N ? ? C DVA 8 C PRO 9 1_555 ? ? ? ? ? ? ? 1.347 ? ? covale11 covale both ? A PRO 9 C ? ? ? 1_555 A SAR 10 N ? ? C PRO 9 C SAR 10 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale12 covale both ? A SAR 10 C ? ? ? 1_555 A MVA 11 N ? ? C SAR 10 C MVA 11 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale13 covale both ? B THR 1 C ? ? ? 1_555 B DVA 2 N ? ? D THR 1 D DVA 2 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale14 covale one ? B THR 1 OG1 ? ? ? 1_555 B MVA 5 C ? ? D THR 1 D MVA 5 1_555 ? ? ? ? ? ? ? 1.372 ? ? covale15 covale both ? B THR 1 N ? ? ? 1_555 B PXZ 6 C0 ? ? D THR 1 D PXZ 6 1_555 ? ? ? ? ? ? ? 1.426 ? ? covale16 covale both ? B DVA 2 C ? ? ? 1_555 B PRO 3 N ? ? D DVA 2 D PRO 3 1_555 ? ? ? ? ? ? ? 1.344 ? ? covale17 covale both ? B PRO 3 C ? ? ? 1_555 B SAR 4 N ? ? D PRO 3 D SAR 4 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale18 covale both ? B SAR 4 C ? ? ? 1_555 B MVA 5 N ? ? D SAR 4 D MVA 5 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale19 covale both ? B PXZ 6 "C0'" ? ? ? 1_555 B THR 7 N ? ? D PXZ 6 D THR 7 1_555 ? ? ? ? ? ? ? 1.425 ? ? covale20 covale both ? B THR 7 C ? ? ? 1_555 B DVA 8 N ? ? D THR 7 D DVA 8 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale21 covale one ? B THR 7 OG1 ? ? ? 1_555 B MVA 11 C ? ? D THR 7 D MVA 11 1_555 ? ? ? ? ? ? ? 1.372 ? ? covale22 covale both ? B DVA 8 C ? ? ? 1_555 B PRO 9 N ? ? D DVA 8 D PRO 9 1_555 ? ? ? ? ? ? ? 1.344 ? ? covale23 covale both ? B PRO 9 C ? ? ? 1_555 B SAR 10 N ? ? D PRO 9 D SAR 10 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale24 covale both ? B SAR 10 C ? ? ? 1_555 B MVA 11 N ? ? D SAR 10 D MVA 11 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale25 covale both ? D THR 1 C ? ? ? 1_555 D DVA 2 N ? ? E THR 1 E DVA 2 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale26 covale one ? D THR 1 OG1 ? ? ? 1_555 D MVA 5 C ? ? E THR 1 E MVA 5 1_555 ? ? ? ? ? ? ? 1.370 ? ? covale27 covale both ? D THR 1 N ? ? ? 1_555 D PXZ 6 C0 ? ? E THR 1 E PXZ 6 1_555 ? ? ? ? ? ? ? 1.427 ? ? covale28 covale both ? D DVA 2 C ? ? ? 1_555 D PRO 3 N ? ? E DVA 2 E PRO 3 1_555 ? ? ? ? ? ? ? 1.348 ? ? covale29 covale both ? D PRO 3 C ? ? ? 1_555 D SAR 4 N ? ? E PRO 3 E SAR 4 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale30 covale both ? D SAR 4 C ? ? ? 1_555 D MVA 5 N ? ? E SAR 4 E MVA 5 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale31 covale both ? D PXZ 6 "C0'" ? ? ? 1_555 D THR 7 N ? ? E PXZ 6 E THR 7 1_555 ? ? ? ? ? ? ? 1.426 ? ? covale32 covale both ? D THR 7 C ? ? ? 1_555 D DVA 8 N ? ? E THR 7 E DVA 8 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale33 covale one ? D THR 7 OG1 ? ? ? 1_555 D MVA 11 C ? ? E THR 7 E MVA 11 1_555 ? ? ? ? ? ? ? 1.370 ? ? covale34 covale both ? D DVA 8 C ? ? ? 1_555 D PRO 9 N ? ? E DVA 8 E PRO 9 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale35 covale both ? D PRO 9 C ? ? ? 1_555 D SAR 10 N ? ? E PRO 9 E SAR 10 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale36 covale both ? D SAR 10 C ? ? ? 1_555 D MVA 11 N ? ? E SAR 10 E MVA 11 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale37 covale both ? E THR 1 C ? ? ? 1_555 E DVA 2 N ? ? F THR 1 F DVA 2 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale38 covale one ? E THR 1 OG1 ? ? ? 1_555 E MVA 5 C ? ? F THR 1 F MVA 5 1_555 ? ? ? ? ? ? ? 1.370 ? ? covale39 covale both ? E THR 1 N ? ? ? 1_555 E PXZ 6 C0 ? ? F THR 1 F PXZ 6 1_555 ? ? ? ? ? ? ? 1.428 ? ? covale40 covale both ? E DVA 2 C ? ? ? 1_555 E PRO 3 N ? ? F DVA 2 F PRO 3 1_555 ? ? ? ? ? ? ? 1.351 ? ? covale41 covale both ? E PRO 3 C ? ? ? 1_555 E SAR 4 N ? ? F PRO 3 F SAR 4 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale42 covale both ? E SAR 4 C ? ? ? 1_555 E MVA 5 N ? ? F SAR 4 F MVA 5 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale43 covale both ? E PXZ 6 "C0'" ? ? ? 1_555 E THR 7 N ? ? F PXZ 6 F THR 7 1_555 ? ? ? ? ? ? ? 1.426 ? ? covale44 covale both ? E THR 7 C ? ? ? 1_555 E DVA 8 N ? ? F THR 7 F DVA 8 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale45 covale one ? E THR 7 OG1 ? ? ? 1_555 E MVA 11 C ? ? F THR 7 F MVA 11 1_555 ? ? ? ? ? ? ? 1.373 ? ? covale46 covale both ? E DVA 8 C ? ? ? 1_555 E PRO 9 N ? ? F DVA 8 F PRO 9 1_555 ? ? ? ? ? ? ? 1.344 ? ? covale47 covale both ? E PRO 9 C ? ? ? 1_555 E SAR 10 N ? ? F PRO 9 F SAR 10 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale48 covale both ? E SAR 10 C ? ? ? 1_555 E MVA 11 N ? ? F SAR 10 F MVA 11 1_555 ? ? ? ? ? ? ? 1.337 ? ? hydrog1 hydrog ? ? C DG 3 N1 ? ? ? 1_555 F DC 6 N3 ? ? A DG 3 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? C DG 3 N2 ? ? ? 1_555 F DC 6 O2 ? ? A DG 3 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? C DG 3 O6 ? ? ? 1_555 F DC 6 N4 ? ? A DG 3 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? C DC 4 N3 ? ? ? 1_555 F DG 5 N1 ? ? A DC 4 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? C DC 4 N4 ? ? ? 1_555 F DG 5 O6 ? ? A DC 4 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? C DC 4 O2 ? ? ? 1_555 F DG 5 N2 ? ? A DC 4 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? C DG 5 N1 ? ? ? 1_555 F DC 4 N3 ? ? A DG 5 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? C DG 5 N2 ? ? ? 1_555 F DC 4 O2 ? ? A DG 5 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? C DG 5 O6 ? ? ? 1_555 F DC 4 N4 ? ? A DG 5 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? C DC 6 N3 ? ? ? 1_555 F DG 3 N1 ? ? A DC 6 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? C DC 6 N4 ? ? ? 1_555 F DG 3 O6 ? ? A DC 6 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? C DC 6 O2 ? ? ? 1_555 F DG 3 N2 ? ? A DC 6 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 SAR A 4 ? . . . . SAR C 4 ? 1_555 . . . . . . . GLY 1 SAR Methylation 'Named protein modification' 2 MVA A 5 ? . . . . MVA C 5 ? 1_555 . . . . . . . VAL 1 MVA Methylation 'Named protein modification' 3 SAR A 10 ? . . . . SAR C 10 ? 1_555 . . . . . . . GLY 1 SAR Methylation 'Named protein modification' 4 MVA A 11 ? . . . . MVA C 11 ? 1_555 . . . . . . . VAL 1 MVA Methylation 'Named protein modification' 5 SAR B 4 ? . . . . SAR D 4 ? 1_555 . . . . . . . GLY 1 SAR Methylation 'Named protein modification' 6 MVA B 5 ? . . . . MVA D 5 ? 1_555 . . . . . . . VAL 1 MVA Methylation 'Named protein modification' 7 SAR B 10 ? . . . . SAR D 10 ? 1_555 . . . . . . . GLY 1 SAR Methylation 'Named protein modification' 8 MVA B 11 ? . . . . MVA D 11 ? 1_555 . . . . . . . VAL 1 MVA Methylation 'Named protein modification' 9 SAR D 4 ? . . . . SAR E 4 ? 1_555 . . . . . . . GLY 1 SAR Methylation 'Named protein modification' 10 MVA D 5 ? . . . . MVA E 5 ? 1_555 . . . . . . . VAL 1 MVA Methylation 'Named protein modification' 11 SAR D 10 ? . . . . SAR E 10 ? 1_555 . . . . . . . GLY 1 SAR Methylation 'Named protein modification' 12 MVA D 11 ? . . . . MVA E 11 ? 1_555 . . . . . . . VAL 1 MVA Methylation 'Named protein modification' 13 SAR E 4 ? . . . . SAR F 4 ? 1_555 . . . . . . . GLY 1 SAR Methylation 'Named protein modification' 14 MVA E 5 ? . . . . MVA F 5 ? 1_555 . . . . . . . VAL 1 MVA Methylation 'Named protein modification' 15 SAR E 10 ? . . . . SAR F 10 ? 1_555 . . . . . . . GLY 1 SAR Methylation 'Named protein modification' 16 MVA E 11 ? . . . . MVA F 11 ? 1_555 . . . . . . . VAL 1 MVA Methylation 'Named protein modification' 17 PXZ A 6 ? . . . . PXZ C 6 ? 1_555 . . . . . . . ? 1 PXZ None 'Non-standard residue' 18 PXZ B 6 ? . . . . PXZ D 6 ? 1_555 . . . . . . . ? 1 PXZ None 'Non-standard residue' 19 PXZ D 6 ? . . . . PXZ E 6 ? 1_555 . . . . . . . ? 1 PXZ None 'Non-standard residue' 20 PXZ E 6 ? . . . . PXZ F 6 ? 1_555 . . . . . . . ? 1 PXZ None 'Non-standard residue' 21 THR A 1 ? MVA A 5 ? THR C 1 ? 1_555 MVA C 5 ? 1_555 OG1 C . . . None 'Non-standard linkage' 22 THR A 1 ? PXZ A 6 ? THR C 1 ? 1_555 PXZ C 6 ? 1_555 N C0 . . . None 'Non-standard linkage' 23 THR A 7 ? MVA A 11 ? THR C 7 ? 1_555 MVA C 11 ? 1_555 OG1 C . . . None 'Non-standard linkage' 24 THR B 1 ? MVA B 5 ? THR D 1 ? 1_555 MVA D 5 ? 1_555 OG1 C . . . None 'Non-standard linkage' 25 THR B 1 ? PXZ B 6 ? THR D 1 ? 1_555 PXZ D 6 ? 1_555 N C0 . . . None 'Non-standard linkage' 26 THR B 7 ? MVA B 11 ? THR D 7 ? 1_555 MVA D 11 ? 1_555 OG1 C . . . None 'Non-standard linkage' 27 THR D 1 ? MVA D 5 ? THR E 1 ? 1_555 MVA E 5 ? 1_555 OG1 C . . . None 'Non-standard linkage' 28 THR D 1 ? PXZ D 6 ? THR E 1 ? 1_555 PXZ E 6 ? 1_555 N C0 . . . None 'Non-standard linkage' 29 THR D 7 ? MVA D 11 ? THR E 7 ? 1_555 MVA E 11 ? 1_555 OG1 C . . . None 'Non-standard linkage' 30 THR E 1 ? MVA E 5 ? THR F 1 ? 1_555 MVA F 5 ? 1_555 OG1 C . . . None 'Non-standard linkage' 31 THR E 1 ? PXZ E 6 ? THR F 1 ? 1_555 PXZ F 6 ? 1_555 N C0 . . . None 'Non-standard linkage' 32 THR E 7 ? MVA E 11 ? THR F 7 ? 1_555 MVA F 11 ? 1_555 OG1 C . . . None 'Non-standard linkage' # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 DVA 2 A . ? DVA 2 C PRO 3 A ? PRO 3 C 1 9.61 2 PRO 3 A . ? PRO 3 C SAR 4 A ? SAR 4 C 1 -1.27 3 DVA 8 A . ? DVA 8 C PRO 9 A ? PRO 9 C 1 7.11 4 PRO 9 A . ? PRO 9 C SAR 10 A ? SAR 10 C 1 0.97 5 DVA 2 B . ? DVA 2 D PRO 3 B ? PRO 3 D 1 8.63 6 PRO 3 B . ? PRO 3 D SAR 4 B ? SAR 4 D 1 -2.53 7 DVA 8 B . ? DVA 8 D PRO 9 B ? PRO 9 D 1 7.21 8 PRO 9 B . ? PRO 9 D SAR 10 B ? SAR 10 D 1 2.48 9 DVA 2 D . ? DVA 2 E PRO 3 D ? PRO 3 E 1 9.04 10 PRO 3 D . ? PRO 3 E SAR 4 D ? SAR 4 E 1 -1.01 11 DVA 8 D . ? DVA 8 E PRO 9 D ? PRO 9 E 1 10.53 12 PRO 9 D . ? PRO 9 E SAR 10 D ? SAR 10 E 1 0.23 13 DVA 2 E . ? DVA 2 F PRO 3 E ? PRO 3 F 1 7.59 14 PRO 3 E . ? PRO 3 F SAR 4 E ? SAR 4 F 1 -2.26 15 DVA 8 E . ? DVA 8 F PRO 9 E ? PRO 9 F 1 11.61 16 PRO 9 E . ? PRO 9 F SAR 10 E ? SAR 10 F 1 0.04 # _pdbx_entry_details.entry_id 9WPJ _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ;ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES) ; _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification Y # 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 OG1 D THR 7 ? ? O D MVA 11 ? ? 1.93 2 1 OG1 D THR 1 ? ? CA D MVA 5 ? ? 2.19 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 DA _pdbx_validate_rmsd_angle.auth_seq_id_1 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 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 DA _pdbx_validate_rmsd_angle.auth_seq_id_2 1 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N9 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 DA _pdbx_validate_rmsd_angle.auth_seq_id_3 1 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 110.20 _pdbx_validate_rmsd_angle.angle_target_value 108.30 _pdbx_validate_rmsd_angle.angle_deviation 1.90 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.30 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_molecule_features.prd_id PRD_000001 _pdbx_molecule_features.name 'Actinomycin D' _pdbx_molecule_features.type Polypeptide _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ) ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000001 A 2 PRD_000001 B 3 PRD_000001 D 4 PRD_000001 E # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 173 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id N _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? D HOH 218 ? 6.02 . 2 1 O ? D HOH 219 ? 7.13 . 3 1 O ? D HOH 220 ? 8.25 . 4 1 O ? A HOH 267 ? 5.81 . 5 1 O ? A HOH 268 ? 6.04 . 6 1 O ? A HOH 269 ? 6.64 . 7 1 O ? A HOH 270 ? 6.81 . 8 1 O ? A HOH 271 ? 6.98 . 9 1 O ? A HOH 272 ? . 7.28 10 1 O ? A HOH 273 ? 7.92 . 11 1 O ? A HOH 274 ? 10.63 . 12 1 O ? E HOH 114 ? 5.98 . 13 1 O ? E HOH 115 ? 6.38 . 14 1 O ? E HOH 116 ? 7.17 . 15 1 O ? F HOH 114 ? 6.28 . 16 1 O ? F HOH 115 ? 8.46 . 17 1 O ? F HOH 116 ? 8.69 . 18 1 O ? F HOH 117 ? 9.59 . 19 1 O ? B HOH 158 ? 5.81 . 20 1 O ? B HOH 159 ? 5.87 . 21 1 O ? B HOH 160 ? 6.08 . 22 1 O ? B HOH 161 ? 6.23 . 23 1 O ? B HOH 162 ? 6.48 . 24 1 O ? B HOH 163 ? 6.52 . 25 1 O ? B HOH 164 ? 6.62 . 26 1 O ? B HOH 165 ? 6.97 . 27 1 O ? B HOH 166 ? 7.09 . 28 1 O ? B HOH 167 ? 7.16 . 29 1 O ? B HOH 168 ? 7.53 . 30 1 O ? B HOH 169 ? 7.61 . 31 1 O ? B HOH 170 ? 7.78 . 32 1 O ? B HOH 171 ? 8.85 . 33 1 O ? B HOH 172 ? 8.92 . 34 1 O ? B HOH 173 ? 9.26 . 35 1 O ? B HOH 174 ? 10.30 . 36 1 O ? B HOH 175 ? 11.21 . 37 1 O ? B HOH 176 ? 11.82 . 38 1 O ? B HOH 177 ? 12.03 . 39 1 O ? B HOH 178 ? 12.25 . 40 1 O ? B HOH 179 ? 13.42 . # 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 DVA N N N N 144 DVA CA C N R 145 DVA CB C N N 146 DVA CG1 C N N 147 DVA CG2 C N N 148 DVA C C N N 149 DVA O O N N 150 DVA OXT O N N 151 DVA H H N N 152 DVA H2 H N N 153 DVA HA H N N 154 DVA HB H N N 155 DVA HG11 H N N 156 DVA HG12 H N N 157 DVA HG13 H N N 158 DVA HG21 H N N 159 DVA HG22 H N N 160 DVA HG23 H N N 161 DVA HXT H N N 162 GOL C1 C N N 163 GOL O1 O N N 164 GOL C2 C N N 165 GOL O2 O N N 166 GOL C3 C N N 167 GOL O3 O N N 168 GOL H11 H N N 169 GOL H12 H N N 170 GOL HO1 H N N 171 GOL H2 H N N 172 GOL HO2 H N N 173 GOL H31 H N N 174 GOL H32 H N N 175 GOL HO3 H N N 176 HOH O O N N 177 HOH H1 H N N 178 HOH H2 H N N 179 MVA N N N N 180 MVA CN C N N 181 MVA CA C N S 182 MVA CB C N N 183 MVA CG1 C N N 184 MVA CG2 C N N 185 MVA C C N N 186 MVA O O N N 187 MVA OXT O N N 188 MVA H H N N 189 MVA HN1 H N N 190 MVA HN2 H N N 191 MVA HN3 H N N 192 MVA HA H N N 193 MVA HB H N N 194 MVA HG11 H N N 195 MVA HG12 H N N 196 MVA HG13 H N N 197 MVA HG21 H N N 198 MVA HG22 H N N 199 MVA HG23 H N N 200 MVA HXT H N N 201 PEG C1 C N N 202 PEG O1 O N N 203 PEG C2 C N N 204 PEG O2 O N N 205 PEG C3 C N N 206 PEG C4 C N N 207 PEG O4 O N N 208 PEG H11 H N N 209 PEG H12 H N N 210 PEG HO1 H N N 211 PEG H21 H N N 212 PEG H22 H N N 213 PEG H31 H N N 214 PEG H32 H N N 215 PEG H41 H N N 216 PEG H42 H N N 217 PEG HO4 H N N 218 PRO N N N N 219 PRO CA C N S 220 PRO C C N N 221 PRO O O N N 222 PRO CB C N N 223 PRO CG C N N 224 PRO CD C N N 225 PRO OXT O N N 226 PRO H H N N 227 PRO HA H N N 228 PRO HB2 H N N 229 PRO HB3 H N N 230 PRO HG2 H N N 231 PRO HG3 H N N 232 PRO HD2 H N N 233 PRO HD3 H N N 234 PRO HXT H N N 235 PXZ C1 C N N 236 PXZ C0 C N N 237 PXZ O1 O N N 238 PXZ C2 C N N 239 PXZ N2 N N N 240 PXZ C3 C N N 241 PXZ O3 O N N 242 PXZ C4 C N N 243 PXZ O5 O N N 244 PXZ C6 C Y N 245 PXZ C7 C Y N 246 PXZ C8 C Y N 247 PXZ C9 C Y N 248 PXZ "C0'" C N N 249 PXZ "O1'" O N N 250 PXZ N10 N N N 251 PXZ C11 C N N 252 PXZ C12 C N N 253 PXZ C13 C Y N 254 PXZ C14 C Y N 255 PXZ C15 C N N 256 PXZ C16 C N N 257 PXZ HN21 H N N 258 PXZ HN22 H N N 259 PXZ H7 H N N 260 PXZ H8 H N N 261 PXZ H151 H N N 262 PXZ H152 H N N 263 PXZ H153 H N N 264 PXZ H161 H N N 265 PXZ H162 H N N 266 PXZ H163 H N N 267 PXZ "OXT'" O N N 268 PXZ OXT O N N 269 PXZ "HXT'" H N N 270 PXZ HXT H N N 271 SAR N N N N 272 SAR CA C N N 273 SAR C C N N 274 SAR O O N N 275 SAR CN C N N 276 SAR OXT O N N 277 SAR H H N N 278 SAR HA2 H N N 279 SAR HA3 H N N 280 SAR HN1 H N N 281 SAR HN2 H N N 282 SAR HN3 H N N 283 SAR HXT H N N 284 THR N N N N 285 THR CA C N S 286 THR C C N N 287 THR O O N N 288 THR CB C N R 289 THR OG1 O N N 290 THR CG2 C N N 291 THR OXT O N N 292 THR H H N N 293 THR H2 H N N 294 THR HA H N N 295 THR HB H N N 296 THR HG1 H N N 297 THR HG21 H N N 298 THR HG22 H N N 299 THR HG23 H N N 300 THR HXT H N N 301 # 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 DVA N CA sing N N 150 DVA N H sing N N 151 DVA N H2 sing N N 152 DVA CA CB sing N N 153 DVA CA C sing N N 154 DVA CA HA sing N N 155 DVA CB CG1 sing N N 156 DVA CB CG2 sing N N 157 DVA CB HB sing N N 158 DVA CG1 HG11 sing N N 159 DVA CG1 HG12 sing N N 160 DVA CG1 HG13 sing N N 161 DVA CG2 HG21 sing N N 162 DVA CG2 HG22 sing N N 163 DVA CG2 HG23 sing N N 164 DVA C O doub N N 165 DVA C OXT sing N N 166 DVA OXT HXT sing N N 167 GOL C1 O1 sing N N 168 GOL C1 C2 sing N N 169 GOL C1 H11 sing N N 170 GOL C1 H12 sing N N 171 GOL O1 HO1 sing N N 172 GOL C2 O2 sing N N 173 GOL C2 C3 sing N N 174 GOL C2 H2 sing N N 175 GOL O2 HO2 sing N N 176 GOL C3 O3 sing N N 177 GOL C3 H31 sing N N 178 GOL C3 H32 sing N N 179 GOL O3 HO3 sing N N 180 HOH O H1 sing N N 181 HOH O H2 sing N N 182 MVA N CN sing N N 183 MVA N CA sing N N 184 MVA N H sing N N 185 MVA CN HN1 sing N N 186 MVA CN HN2 sing N N 187 MVA CN HN3 sing N N 188 MVA CA CB sing N N 189 MVA CA C sing N N 190 MVA CA HA sing N N 191 MVA CB CG1 sing N N 192 MVA CB CG2 sing N N 193 MVA CB HB sing N N 194 MVA CG1 HG11 sing N N 195 MVA CG1 HG12 sing N N 196 MVA CG1 HG13 sing N N 197 MVA CG2 HG21 sing N N 198 MVA CG2 HG22 sing N N 199 MVA CG2 HG23 sing N N 200 MVA C O doub N N 201 MVA C OXT sing N N 202 MVA OXT HXT sing N N 203 PEG C1 O1 sing N N 204 PEG C1 C2 sing N N 205 PEG C1 H11 sing N N 206 PEG C1 H12 sing N N 207 PEG O1 HO1 sing N N 208 PEG C2 O2 sing N N 209 PEG C2 H21 sing N N 210 PEG C2 H22 sing N N 211 PEG O2 C3 sing N N 212 PEG C3 C4 sing N N 213 PEG C3 H31 sing N N 214 PEG C3 H32 sing N N 215 PEG C4 O4 sing N N 216 PEG C4 H41 sing N N 217 PEG C4 H42 sing N N 218 PEG O4 HO4 sing N N 219 PRO N CA sing N N 220 PRO N CD sing N N 221 PRO N H sing N N 222 PRO CA C sing N N 223 PRO CA CB sing N N 224 PRO CA HA sing N N 225 PRO C O doub N N 226 PRO C OXT sing N N 227 PRO CB CG sing N N 228 PRO CB HB2 sing N N 229 PRO CB HB3 sing N N 230 PRO CG CD sing N N 231 PRO CG HG2 sing N N 232 PRO CG HG3 sing N N 233 PRO CD HD2 sing N N 234 PRO CD HD3 sing N N 235 PRO OXT HXT sing N N 236 PXZ C1 C0 sing N N 237 PXZ C1 C2 doub N N 238 PXZ C1 C11 sing N N 239 PXZ C0 O1 doub N N 240 PXZ C2 N2 sing N N 241 PXZ C2 C3 sing N N 242 PXZ N2 HN21 sing N N 243 PXZ N2 HN22 sing N N 244 PXZ C3 O3 doub N N 245 PXZ C3 C4 sing N N 246 PXZ C4 C12 doub N N 247 PXZ C4 C15 sing N N 248 PXZ O5 C12 sing N N 249 PXZ O5 C13 sing N N 250 PXZ C6 C7 doub Y N 251 PXZ C6 C13 sing Y N 252 PXZ C6 C16 sing N N 253 PXZ C7 C8 sing Y N 254 PXZ C7 H7 sing N N 255 PXZ C8 C9 doub Y N 256 PXZ C8 H8 sing N N 257 PXZ C9 "C0'" sing N N 258 PXZ C9 C14 sing Y N 259 PXZ "C0'" "O1'" doub N N 260 PXZ N10 C11 doub N N 261 PXZ N10 C14 sing N N 262 PXZ C11 C12 sing N N 263 PXZ C13 C14 doub Y N 264 PXZ C15 H151 sing N N 265 PXZ C15 H152 sing N N 266 PXZ C15 H153 sing N N 267 PXZ C16 H161 sing N N 268 PXZ C16 H162 sing N N 269 PXZ C16 H163 sing N N 270 PXZ "C0'" "OXT'" sing N N 271 PXZ C0 OXT sing N N 272 PXZ "OXT'" "HXT'" sing N N 273 PXZ OXT HXT sing N N 274 SAR N CA sing N N 275 SAR N CN sing N N 276 SAR N H sing N N 277 SAR CA C sing N N 278 SAR CA HA2 sing N N 279 SAR CA HA3 sing N N 280 SAR C O doub N N 281 SAR C OXT sing N N 282 SAR CN HN1 sing N N 283 SAR CN HN2 sing N N 284 SAR CN HN3 sing N N 285 SAR OXT HXT sing N N 286 THR N CA sing N N 287 THR N H sing N N 288 THR N H2 sing N N 289 THR CA C sing N N 290 THR CA CB sing N N 291 THR CA HA sing N N 292 THR C O doub N N 293 THR C OXT sing N N 294 THR CB OG1 sing N N 295 THR CB CG2 sing N N 296 THR CB HB sing N N 297 THR OG1 HG1 sing N N 298 THR CG2 HG21 sing N N 299 THR CG2 HG22 sing N N 300 THR CG2 HG23 sing N N 301 THR OXT HXT sing N N 302 # _ndb_struct_conf_na.entry_id 9WPJ _ndb_struct_conf_na.feature '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 C DG 3 1_555 F DC 6 1_555 -0.358 -0.087 0.477 15.160 16.925 2.245 1 A_DG3:DC6_B A 3 ? B 6 ? 19 1 1 C DC 4 1_555 F DG 5 1_555 0.317 -0.184 0.678 -5.455 17.335 3.624 2 A_DC4:DG5_B A 4 ? B 5 ? 19 1 1 C DG 5 1_555 F DC 4 1_555 -0.349 -0.180 0.703 7.838 15.616 3.512 3 A_DG5:DC4_B A 5 ? B 4 ? 19 1 1 C DC 6 1_555 F DG 3 1_555 0.540 -0.054 0.440 -14.900 18.213 2.919 4 A_DC6:DG3_B A 6 ? B 3 ? 19 1 # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 C _ndb_struct_na_base_pair_step.i_label_comp_id_1 DC _ndb_struct_na_base_pair_step.i_label_seq_id_1 4 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 F _ndb_struct_na_base_pair_step.j_label_comp_id_1 DG _ndb_struct_na_base_pair_step.j_label_seq_id_1 5 _ndb_struct_na_base_pair_step.j_symmetry_1 1_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 C _ndb_struct_na_base_pair_step.i_label_comp_id_2 DG _ndb_struct_na_base_pair_step.i_label_seq_id_2 5 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 F _ndb_struct_na_base_pair_step.j_label_comp_id_2 DC _ndb_struct_na_base_pair_step.j_label_seq_id_2 4 _ndb_struct_na_base_pair_step.j_symmetry_2 1_555 _ndb_struct_na_base_pair_step.shift -0.135 _ndb_struct_na_base_pair_step.slide 2.022 _ndb_struct_na_base_pair_step.rise 3.366 _ndb_struct_na_base_pair_step.tilt -0.119 _ndb_struct_na_base_pair_step.roll 27.912 _ndb_struct_na_base_pair_step.twist 6.805 _ndb_struct_na_base_pair_step.x_displacement -5.615 _ndb_struct_na_base_pair_step.y_displacement 0.232 _ndb_struct_na_base_pair_step.helical_rise 2.769 _ndb_struct_na_base_pair_step.inclination 76.567 _ndb_struct_na_base_pair_step.tip 0.327 _ndb_struct_na_base_pair_step.helical_twist 28.714 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_DC4DG5:DC4DG5_BB _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 4 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 B _ndb_struct_na_base_pair_step.j_auth_seq_id_1 5 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 5 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 B _ndb_struct_na_base_pair_step.j_auth_seq_id_2 4 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Ministry of Science and Technology (MoST, Taiwan)' Taiwan 113-2311-B-005-006-MY3 1 'Ministry of Science and Technology (MoST, Taiwan)' Taiwan 113-2311-M-005-016-MY3 2 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.details 'Ideal B form DNA' # _atom_sites.entry_id 9WPJ _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.012718 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.007904 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022276 _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] 0.028238 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O P # loop_ #