data_7ZKA # _model_server_result.job_id PXJtdxW7AxdLYlXXMJxwdA _model_server_result.datetime_utc '2025-02-05 05:55:01' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7zka # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1401}' # _entry.id 7ZKA # _exptl.entry_id 7ZKA _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 494.634 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4~{S},11~{S},18~{S})-4,11-dimethyl-18-(sulfanylmethyl)-6,13,20-trithia-3,10,17,22,23,24-hexazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7ZKA _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZKA _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A SG CYS 978 A CYS 978 1_555 B S04 JIZ . A JIZ 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc1 A OG SER 430 A SER 430 1_555 D MG MG . A MG 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc2 A OE1 GLN 471 A GLN 471 1_555 D MG MG . A MG 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc3 A OG SER 1073 A SER 1073 1_555 F MG MG . A MG 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc4 A OE1 GLN 1114 A GLN 1114 1_555 F MG MG . A MG 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc5 C O1G ATP . A ATP 1402 1_555 D MG MG . A MG 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc6 C O2B ATP . A ATP 1402 1_555 D MG MG . A MG 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc7 D MG MG . A MG 1403 1_555 K O HOH . A HOH 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc8 D MG MG . A MG 1403 1_555 K O HOH . A HOH 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc9 E O2G ATP . A ATP 1404 1_555 F MG MG . A MG 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc10 E O2B ATP . A ATP 1404 1_555 F MG MG . A MG 1405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc11 F MG MG . A MG 1405 1_555 K O HOH . A HOH 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc12 F MG MG . A MG 1405 1_555 K O HOH . A HOH 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? # _chem_comp.formula 'C18 H18 N6 O3 S4' _chem_comp.formula_weight 494.634 _chem_comp.id JIZ _chem_comp.mon_nstd_flag . _chem_comp.name (4~{S},11~{S},18~{S})-4,11-dimethyl-18-(sulfanylmethyl)-6,13,20-trithia-3,10,17,22,23,24-hexazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag S03 C14 JIZ sing 222 n y S03 C12 JIZ sing 223 n y C17 C11 JIZ sing 224 n n C14 C13 JIZ doub 225 n y C11 C12 JIZ sing 226 n n C11 N05 JIZ sing 227 n n C12 N06 JIZ doub 228 n y O02 C10 JIZ doub 229 n n N05 C10 JIZ sing 230 n n C13 N06 JIZ sing 231 n y C13 C15 JIZ sing 232 n n C10 C08 JIZ sing 233 n n O03 C15 JIZ doub 234 n n C15 N01 JIZ sing 235 n n C08 C09 JIZ doub 236 n y C08 N04 JIZ sing 237 n y C09 S02 JIZ sing 238 n y N01 C01 JIZ sing 239 n n N04 C07 JIZ doub 240 n y S02 C07 JIZ sing 241 n y S04 C18 JIZ sing 242 n n C01 C18 JIZ sing 243 n n C01 C02 JIZ sing 244 n n C07 C06 JIZ sing 245 n n N02 C02 JIZ doub 246 n y N02 C03 JIZ sing 247 n y C02 S01 JIZ sing 248 n y N03 C06 JIZ sing 249 n n N03 C05 JIZ sing 250 n n C06 C16 JIZ sing 251 n n C03 C05 JIZ sing 252 n n C03 C04 JIZ doub 253 n y S01 C04 JIZ sing 254 n y C05 O01 JIZ doub 255 n n C17 H1 JIZ sing 256 n n C17 H2 JIZ sing 257 n n C17 H3 JIZ sing 258 n n C01 H4 JIZ sing 259 n n C04 H5 JIZ sing 260 n n C06 H6 JIZ sing 261 n n C09 H7 JIZ sing 262 n n C11 H8 JIZ sing 263 n n C14 H9 JIZ sing 264 n n C16 H11 JIZ sing 265 n n C16 H12 JIZ sing 266 n n C18 H13 JIZ sing 267 n n C18 H14 JIZ sing 268 n n N01 H15 JIZ sing 269 n n N03 H16 JIZ sing 270 n n N05 H17 JIZ sing 271 n n S04 H18 JIZ sing 272 n n C16 H10 JIZ sing 273 n n # _atom_sites.entry_id 7ZKA _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code B 2 JIZ A 1 1401 2000 JIZ LIG . C 3 ATP A 1 1402 2001 ATP ATP . D 4 MG A 1 1403 2002 MG MG . E 3 ATP A 1 1404 2005 ATP ATP . F 4 MG A 1 1405 2006 MG MG . G 5 LMN A 1 1406 2010 LMN LMN . H 6 Y01 A 1 1407 2013 Y01 Y01 . I 6 Y01 A 1 1408 2014 Y01 Y01 . J 6 Y01 A 1 1409 2015 Y01 Y01 . K 7 HOH A 1 1501 2003 HOH HOH . K 7 HOH A 2 1502 2004 HOH HOH . K 7 HOH A 3 1503 2007 HOH HOH . K 7 HOH A 4 1504 2008 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C10 JIZ . . . B 2 116.451 118.28 145.042 1 0 ? C10 JIZ 1401 A 1 HETATM 2 C C13 JIZ . . . B 2 116.58 116.788 139.484 1 0 ? C13 JIZ 1401 A 1 HETATM 3 C C15 JIZ . . . B 2 115.989 117.519 138.283 1 0 ? C15 JIZ 1401 A 1 HETATM 4 C C17 JIZ . . . B 2 115.943 115.352 143.931 1 0 ? C17 JIZ 1401 A 1 HETATM 5 C C01 JIZ . . . B 2 114.361 119.322 137.499 1 0 ? C01 JIZ 1401 A 1 HETATM 6 C C02 JIZ . . . B 2 113.847 120.598 138.159 1 0 ? C02 JIZ 1401 A 1 HETATM 7 C C03 JIZ . . . B 2 113.415 122.319 139.804 1 0 ? C03 JIZ 1401 A 1 HETATM 8 C C04 JIZ . . . B 2 112.709 122.773 138.537 1 0 ? C04 JIZ 1401 A 1 HETATM 9 C C05 JIZ . . . B 2 113.468 123.029 141.155 1 0 ? C05 JIZ 1401 A 1 HETATM 10 C C06 JIZ . . . B 2 114.01 122.815 143.646 1 0 ? C06 JIZ 1401 A 1 HETATM 11 C C07 JIZ . . . B 2 114.802 121.8 144.46 1 0 ? C07 JIZ 1401 A 1 HETATM 12 C C08 JIZ . . . B 2 115.95 119.715 145.165 1 0 ? C08 JIZ 1401 A 1 HETATM 13 C C09 JIZ . . . B 2 116.145 120.637 146.276 1 0 ? C09 JIZ 1401 A 1 HETATM 14 C C11 JIZ . . . B 2 116.948 116.369 143.404 1 0 ? C11 JIZ 1401 A 1 HETATM 15 C C12 JIZ . . . B 2 116.992 116.296 141.883 1 0 ? C12 JIZ 1401 A 1 HETATM 16 C C14 JIZ . . . B 2 117.494 115.651 139.479 1 0 ? C14 JIZ 1401 A 1 HETATM 17 C C16 JIZ . . . B 2 112.618 122.975 144.249 1 0 ? C16 JIZ 1401 A 1 HETATM 18 C C18 JIZ . . . B 2 113.194 118.534 136.91 1 0 ? C18 JIZ 1401 A 1 HETATM 19 N N01 JIZ . . . B 2 114.997 118.546 138.545 1 0 ? N01 JIZ 1401 A 1 HETATM 20 N N02 JIZ . . . B 2 114.133 120.884 139.468 1 0 ? N02 JIZ 1401 A 1 HETATM 21 N N03 JIZ . . . B 2 113.909 122.263 142.308 1 0 ? N03 JIZ 1401 A 1 HETATM 22 N N04 JIZ . . . B 2 115.099 120.47 144.017 1 0 ? N04 JIZ 1401 A 1 HETATM 23 N N05 JIZ . . . B 2 116.498 117.712 143.707 1 0 ? N05 JIZ 1401 A 1 HETATM 24 N N06 JIZ . . . B 2 116.274 117.187 141.019 1 0 ? N06 JIZ 1401 A 1 HETATM 25 O O01 JIZ . . . B 2 113.165 124.169 141.254 1 0 ? O01 JIZ 1401 A 1 HETATM 26 O O02 JIZ . . . B 2 116.784 117.662 145.996 1 0 ? O02 JIZ 1401 A 1 HETATM 27 O O03 JIZ . . . B 2 116.331 117.263 137.178 1 0 ? O03 JIZ 1401 A 1 HETATM 28 S S01 JIZ . . . B 2 112.979 121.663 137.45 1 0 ? S01 JIZ 1401 A 1 HETATM 29 S S02 JIZ . . . B 2 115.442 121.985 145.903 1 0 ? S02 JIZ 1401 A 1 HETATM 30 S S03 JIZ . . . B 2 117.803 115.279 140.969 1 0 ? S03 JIZ 1401 A 1 HETATM 31 S S04 JIZ . . . B 2 112.008 118.134 138.227 1 0 ? S04 JIZ 1401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #