data_8VZK # _model_server_result.job_id RSBkho2vITbSpFx3kJln1A _model_server_result.datetime_utc '2025-03-04 09:24:45' _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 8vzk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 8VZK # _exptl.entry_id 8VZK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.314 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'THIAMINE DIPHOSPHATE' _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 8VZK _cell.length_a 111.327 _cell.length_b 111.327 _cell.length_c 193.164 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VZK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,L,M,N _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -64.388 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 I 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 metalc ? metalc1 A OD1 ASP 446 A ASP 448 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc2 A OD1 ASN 473 A ASN 475 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc3 A O GLY 475 A GLY 477 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc4 C O2A TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc5 C O1B TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 C O2B TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc7 B OD1 ASP 446 B ASP 448 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 B OD1 ASN 473 B ASN 475 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc9 I O2A TPP . B TPP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc10 I O1B TPP . B TPP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? # _chem_comp.formula 'C12 H19 N4 O7 P2 S 1' _chem_comp.formula_weight 425.314 _chem_comp.id TPP _chem_comp.mon_nstd_flag . _chem_comp.name 'THIAMINE DIPHOSPHATE' _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 N1' C2' TPP doub 375 n y N1' C6' TPP sing 376 n y C2' CM2 TPP sing 377 n n C2' N3' TPP sing 378 n y CM2 HM21 TPP sing 379 n n CM2 HM22 TPP sing 380 n n CM2 HM23 TPP sing 381 n n N3' C4' TPP doub 382 n y C4' N4' TPP sing 383 n n C4' C5' TPP sing 384 n y N4' HN41 TPP sing 385 n n N4' HN42 TPP sing 386 n n C5' C6' TPP doub 387 n y C5' C7' TPP sing 388 n n C6' H6' TPP sing 389 n n C7' N3 TPP sing 390 n n C7' "H7'1" TPP sing 391 n n C7' "H7'2" TPP sing 392 n n N3 C2 TPP doub 393 n y N3 C4 TPP sing 394 n y C2 S1 TPP sing 395 n y C2 H2 TPP sing 396 n n S1 C5 TPP sing 397 n y C5 C4 TPP doub 398 n y C5 C6 TPP sing 399 n n C4 CM4 TPP sing 400 n n CM4 HM41 TPP sing 401 n n CM4 HM42 TPP sing 402 n n CM4 HM43 TPP sing 403 n n C6 C7 TPP sing 404 n n C6 H61 TPP sing 405 n n C6 H62 TPP sing 406 n n C7 O7 TPP sing 407 n n C7 H71 TPP sing 408 n n C7 H72 TPP sing 409 n n O7 PA TPP sing 410 n n PA O1A TPP doub 411 n n PA O2A TPP sing 412 n n PA O3A TPP sing 413 n n O2A HOA2 TPP sing 414 n n O3A PB TPP sing 415 n n PB O1B TPP doub 416 n n PB O2B TPP sing 417 n n PB O3B TPP sing 418 n n O2B HOB2 TPP sing 419 n n O3B HOB3 TPP sing 420 n n # _atom_sites.entry_id 8VZK _atom_sites.fract_transf_matrix[1][1] 0.008983 _atom_sites.fract_transf_matrix[1][2] 0.005186 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010372 _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] 0.005177 _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 C 2 TPP A 1 601 601 TPP TPP . D 3 ADP A 1 602 602 ADP ADP . E 4 MG A 1 603 605 MG MG . F 5 EDO A 1 604 611 EDO EDO . G 5 EDO A 1 605 612 EDO EDO . H 6 PEG A 1 606 613 PEG PEG . I 2 TPP B 1 601 601 TPP TPP . J 3 ADP B 1 602 602 ADP ADP . K 4 MG B 1 603 605 MG MG . L 5 EDO B 1 604 611 EDO EDO . M 7 HOH A 1 701 4 HOH HOH . N 7 HOH B 1 701 3 HOH HOH . N 7 HOH B 2 702 2 HOH HOH . N 7 HOH B 3 703 1 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 N N1' TPP . . . C 2 62.885 -4.675 -11.108 1 47.23 ? N1' TPP 601 A 1 HETATM 2 C C2' TPP . . . C 2 62.232 -5.699 -11.677 1 49.66 ? C2' TPP 601 A 1 HETATM 3 C CM2 TPP . . . C 2 60.796 -5.484 -12.027 1 51.35 ? CM2 TPP 601 A 1 HETATM 4 N N3' TPP . . . C 2 62.756 -6.897 -11.957 1 52.36 ? N3' TPP 601 A 1 HETATM 5 C C4' TPP . . . C 2 64.048 -7.105 -11.649 1 50.91 ? C4' TPP 601 A 1 HETATM 6 N N4' TPP . . . C 2 64.555 -8.308 -11.934 1 52.28 ? N4' TPP 601 A 1 HETATM 7 C C5' TPP . . . C 2 64.83 -6.08 -11.042 1 51.12 ? C5' TPP 601 A 1 HETATM 8 C C6' TPP . . . C 2 64.169 -4.896 -10.806 1 50.08 ? C6' TPP 601 A 1 HETATM 9 C C7' TPP . . . C 2 66.276 -6.258 -10.666 1 57.39 ? C7' TPP 601 A 1 HETATM 10 N N3 TPP . . . C 2 66.466 -7.196 -9.534 1 60.55 ? N3 TPP 601 A 1 HETATM 11 C C2 TPP . . . C 2 66.768 -8.471 -9.681 1 63.89 ? C2 TPP 601 A 1 HETATM 12 S S1 TPP . . . C 2 66.901 -9.267 -8.213 1 61.05 ? S1 TPP 601 A 1 HETATM 13 C C5 TPP . . . C 2 66.53 -7.819 -7.348 1 61.6 ? C5 TPP 601 A 1 HETATM 14 C C4 TPP . . . C 2 66.319 -6.796 -8.207 1 56.38 ? C4 TPP 601 A 1 HETATM 15 C CM4 TPP . . . C 2 65.975 -5.387 -7.869 1 56.75 ? CM4 TPP 601 A 1 HETATM 16 C C6 TPP . . . C 2 66.468 -7.801 -5.847 1 61.34 ? C6 TPP 601 A 1 HETATM 17 C C7 TPP . . . C 2 67.479 -8.717 -5.198 1 62.2 ? C7 TPP 601 A 1 HETATM 18 O O7 TPP . . . C 2 67.44 -8.499 -3.766 1 72.31 ? O7 TPP 601 A 1 HETATM 19 P PA TPP . . . C 2 66.886 -9.541 -2.723 1 65.63 ? PA TPP 601 A 1 HETATM 20 O O1A TPP . . . C 2 65.608 -10.122 -3.187 1 62.8 ? O1A TPP 601 A 1 HETATM 21 O O2A TPP . . . C 2 66.83 -8.856 -1.363 1 65.96 ? O2A TPP 601 A 1 HETATM 22 O O3A TPP . . . C 2 68.043 -10.626 -2.648 1 61.32 ? O3A TPP 601 A 1 HETATM 23 P PB TPP . . . C 2 69.365 -10.931 -1.826 1 66.95 ? PB TPP 601 A 1 HETATM 24 O O1B TPP . . . C 2 70.056 -9.668 -1.433 1 71.48 ? O1B TPP 601 A 1 HETATM 25 O O2B TPP . . . C 2 68.887 -11.768 -0.635 1 73.53 ? O2B TPP 601 A 1 HETATM 26 O O3B TPP . . . C 2 70.192 -11.824 -2.755 1 69.61 ? O3B TPP 601 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #