data_8JV7 # _model_server_result.job_id hGOmrYkrOf23R1XvgnJzYQ _model_server_result.datetime_utc '2024-10-20 05:47:00' _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 8jv7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":403}' # _entry.id 8JV7 # _exptl.entry_id 8JV7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 511.378 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-[(E)-[4-methanoyl-6-methyl-5-oxidanyl-3-(phosphonooxymethyl)pyridin-2-yl]diazenyl]benzene-1,3-disulfonic acid' _entity.pdbx_number_of_molecules 3 _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 8JV7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JV7 _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 I N N ? 3 L N 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 disulf ? disulf1 A SG CYS 99 A CYS 119 1_555 A SG CYS 148 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 109 A CYS 129 1_555 A SG CYS 132 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 115 A CYS 135 1_555 A SG CYS 142 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 196 A CYS 216 1_555 A SG CYS 206 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 240 A CYS 260 1_555 A SG CYS 249 A CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 99 B CYS 119 1_555 B SG CYS 148 B CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 109 B CYS 129 1_555 B SG CYS 132 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 115 B CYS 135 1_555 B SG CYS 142 B CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 B SG CYS 196 B CYS 216 1_555 B SG CYS 206 B CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 240 B CYS 260 1_555 B SG CYS 249 B CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 C SG CYS 99 C CYS 119 1_555 C SG CYS 148 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 C SG CYS 109 C CYS 129 1_555 C SG CYS 132 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf13 C SG CYS 115 C CYS 135 1_555 C SG CYS 142 C CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf14 C SG CYS 196 C CYS 216 1_555 C SG CYS 206 C CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 C SG CYS 240 C CYS 260 1_555 C SG CYS 249 C CYS 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 167 A ASN 187 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 193 A ASN 213 1_555 E C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 B ND2 ASN 167 B ASN 187 1_555 G C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B ND2 ASN 193 B ASN 213 1_555 H C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 C ND2 ASN 167 C ASN 187 1_555 J C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 C ND2 ASN 193 C ASN 213 1_555 K C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C14 H14 N3 O12 P S2' _chem_comp.formula_weight 511.378 _chem_comp.id UO6 _chem_comp.mon_nstd_flag . _chem_comp.name '4-[(E)-[4-methanoyl-6-methyl-5-oxidanyl-3-(phosphonooxymethyl)pyridin-2-yl]diazenyl]benzene-1,3-disulfonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Ppads # 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 O17 S16 UO6 doub 388 n n O19 S16 UO6 doub 389 n n S16 O18 UO6 sing 390 n n S16 C13 UO6 sing 391 n n C13 C12 UO6 doub 392 n y C13 C14 UO6 sing 393 n y C12 C11 UO6 sing 394 n y O21 S20 UO6 doub 395 n n C14 C15 UO6 doub 396 n y O22 S20 UO6 doub 397 n n C11 S20 UO6 sing 398 n n C11 C10 UO6 doub 399 n y C15 C10 UO6 sing 400 n y S20 O23 UO6 sing 401 n n C10 N09 UO6 sing 402 n n N09 N08 UO6 doub 403 n n N08 C06 UO6 sing 404 n n O29 P26 UO6 doub 405 n n C06 N07 UO6 doub 406 n y C06 C05 UO6 sing 407 n y N07 C02 UO6 sing 408 n y C24 C05 UO6 sing 409 n n C24 O25 UO6 sing 410 n n C05 C04 UO6 doub 411 n y C02 C01 UO6 sing 412 n n C02 C03 UO6 doub 413 n y O28 P26 UO6 sing 414 n n P26 O25 UO6 sing 415 n n P26 O27 UO6 sing 416 n n C04 C03 UO6 sing 417 n y C04 C30 UO6 sing 418 n n C03 O32 UO6 sing 419 n n C30 O31 UO6 doub 420 n n C01 H1 UO6 sing 421 n n C01 H2 UO6 sing 422 n n C01 H3 UO6 sing 423 n n C12 H4 UO6 sing 424 n n C14 H5 UO6 sing 425 n n C15 H6 UO6 sing 426 n n C24 H7 UO6 sing 427 n n C24 H8 UO6 sing 428 n n C30 H9 UO6 sing 429 n n O27 H10 UO6 sing 430 n n O28 H11 UO6 sing 431 n n O32 H12 UO6 sing 432 n n O18 H13 UO6 sing 433 n n O23 H14 UO6 sing 434 n n # _atom_sites.entry_id 8JV7 _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 D 2 NAG A 1 401 401 NAG NAG . E 2 NAG A 1 402 402 NAG NAG . F 3 UO6 A 1 403 403 UO6 PPA . G 2 NAG B 1 401 401 NAG NAG . H 2 NAG B 1 402 402 NAG NAG . I 3 UO6 B 1 403 403 UO6 PPA . J 2 NAG C 1 401 401 NAG NAG . K 2 NAG C 1 402 402 NAG NAG . L 3 UO6 C 1 403 403 UO6 PPA . M 4 HOH A 1 501 404 HOH HOH . N 4 HOH B 1 501 404 HOH HOH . O 4 HOH C 1 501 404 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 C01 UO6 . . . I 3 84.685 122.539 125.398 1 158.3 ? C01 UO6 403 B 1 HETATM 2 C C02 UO6 . . . I 3 85.379 121.192 125.213 1 158.3 ? C02 UO6 403 B 1 HETATM 3 C C03 UO6 . . . I 3 86.671 121.015 125.676 1 158.3 ? C03 UO6 403 B 1 HETATM 4 C C04 UO6 . . . I 3 87.304 119.793 125.51 1 158.3 ? C04 UO6 403 B 1 HETATM 5 C C05 UO6 . . . I 3 86.606 118.776 124.873 1 158.3 ? C05 UO6 403 B 1 HETATM 6 C C06 UO6 . . . I 3 85.315 119.029 124.437 1 158.3 ? C06 UO6 403 B 1 HETATM 7 C C10 UO6 . . . I 3 82.692 117.131 122.715 1 158.3 ? C10 UO6 403 B 1 HETATM 8 C C11 UO6 . . . I 3 81.401 117.376 122.274 1 158.3 ? C11 UO6 403 B 1 HETATM 9 C C12 UO6 . . . I 3 80.684 116.374 121.64 1 158.3 ? C12 UO6 403 B 1 HETATM 10 C C13 UO6 . . . I 3 81.257 115.127 121.451 1 158.3 ? C13 UO6 403 B 1 HETATM 11 C C14 UO6 . . . I 3 82.547 114.882 121.892 1 158.3 ? C14 UO6 403 B 1 HETATM 12 C C15 UO6 . . . I 3 83.265 115.884 122.526 1 158.3 ? C15 UO6 403 B 1 HETATM 13 C C24 UO6 . . . I 3 87.244 117.406 124.657 1 158.3 ? C24 UO6 403 B 1 HETATM 14 C C30 UO6 . . . I 3 88.728 119.576 126.012 1 158.3 ? C30 UO6 403 B 1 HETATM 15 N N07 UO6 . . . I 3 84.742 120.204 124.612 1 158.3 ? N07 UO6 403 B 1 HETATM 16 N N08 UO6 . . . I 3 84.572 117.973 123.77 1 158.3 ? N08 UO6 403 B 1 HETATM 17 N N09 UO6 . . . I 3 83.441 118.184 123.382 1 158.3 ? N09 UO6 403 B 1 HETATM 18 O O17 UO6 . . . I 3 79.558 114.349 119.43 1 158.3 ? O17 UO6 403 B 1 HETATM 19 O O18 UO6 . . . I 3 79.184 113.32 121.488 1 158.3 ? O18 UO6 403 B 1 HETATM 20 O O19 UO6 . . . I 3 81.235 112.681 120.223 1 158.3 ? O19 UO6 403 B 1 HETATM 21 O O21 UO6 . . . I 3 81.459 120.092 121.846 1 158.3 ? O21 UO6 403 B 1 HETATM 22 O O22 UO6 . . . I 3 79.332 119.127 121.805 1 158.3 ? O22 UO6 403 B 1 HETATM 23 O O23 UO6 . . . I 3 80.501 119.291 124.002 1 158.3 ? O23 UO6 403 B 1 HETATM 24 O O25 UO6 . . . I 3 86.868 116.568 125.713 1 158.3 ? O25 UO6 403 B 1 HETATM 25 O O27 UO6 . . . I 3 86.736 114.249 126.839 1 158.3 ? O27 UO6 403 B 1 HETATM 26 O O28 UO6 . . . I 3 88.631 114.722 125.336 1 158.3 ? O28 UO6 403 B 1 HETATM 27 O O29 UO6 . . . I 3 86.372 114.399 124.405 1 158.3 ? O29 UO6 403 B 1 HETATM 28 O O31 UO6 . . . I 3 89.309 120.46 126.548 1 158.3 ? O31 UO6 403 B 1 HETATM 29 O O32 UO6 . . . I 3 87.34 122.069 126.313 1 158.3 ? O32 UO6 403 B 1 HETATM 30 P P26 UO6 . . . I 3 87.157 114.951 125.57 1 158.3 ? P26 UO6 403 B 1 HETATM 31 S S16 UO6 . . . I 3 80.317 113.813 120.62 1 158.3 ? S16 UO6 403 B 1 HETATM 32 S S20 UO6 . . . I 3 80.654 119.011 122.526 1 158.3 ? S20 UO6 403 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #