data_8P5T # _model_server_result.job_id 980A1cacCa-X95wM3590Ug _model_server_result.datetime_utc '2024-10-19 07:36:57' _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 8p5t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1303}' # _entry.id 8P5T # _exptl.entry_id 8P5T _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 425.314 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'THIAMINE DIPHOSPHATE' _entity.pdbx_number_of_molecules 6 _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 8P5T _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8P5T _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,P,Q,R,S,T,U,V,W,X _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 ? 4 I N N ? 4 L N N ? 4 O N N ? 4 R N N ? 4 U N N ? 4 X 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 647 A ASP 645 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc2 A OD1 ASN 680 A ASN 678 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc3 A O ILE 682 A ILE 680 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 G MG MG . A MG 1301 1_555 I O2B TPP . A TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc5 G MG MG . A MG 1301 1_555 I O1A TPP . A TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc6 B OD1 ASP 647 B ASP 645 1_555 J MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc7 B OD1 ASN 680 B ASN 678 1_555 J MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc8 B O ILE 682 B ILE 680 1_555 J MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc9 J MG MG . B MG 1301 1_555 L O2A TPP . B TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc10 J MG MG . B MG 1301 1_555 L O2B TPP . B TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc11 C OD1 ASP 647 C ASP 645 1_555 M MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc12 C OD1 ASN 680 C ASN 678 1_555 M MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc13 C O ILE 682 C ILE 680 1_555 M MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc14 M MG MG . C MG 1301 1_555 O O2B TPP . C TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc15 M MG MG . C MG 1301 1_555 O O1A TPP . C TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc16 D OD1 ASP 647 D ASP 645 1_555 P MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc17 D OD1 ASN 680 D ASN 678 1_555 P MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc18 D O ILE 682 D ILE 680 1_555 P MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc19 P MG MG . D MG 1301 1_555 R O2A TPP . D TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc20 P MG MG . D MG 1301 1_555 R O2B TPP . D TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc21 E OD1 ASP 647 E ASP 645 1_555 S MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc22 E OD1 ASN 680 E ASN 678 1_555 S MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc23 E O ILE 682 E ILE 680 1_555 S MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc24 S MG MG . E MG 1301 1_555 U O2B TPP . E TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc25 S MG MG . E MG 1301 1_555 U O1A TPP . E TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc26 F OD1 ASP 647 F ASP 645 1_555 V MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc27 F OD1 ASN 680 F ASN 678 1_555 V MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc28 F O ILE 682 F ILE 680 1_555 V MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc29 V MG MG . F MG 1301 1_555 X O2B TPP . F TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc30 V MG MG . F MG 1301 1_555 X O2A TPP . F TPP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? # _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 395 n y N1' C6' TPP sing 396 n y C2' CM2 TPP sing 397 n n C2' N3' TPP sing 398 n y CM2 HM21 TPP sing 399 n n CM2 HM22 TPP sing 400 n n CM2 HM23 TPP sing 401 n n N3' C4' TPP doub 402 n y C4' N4' TPP sing 403 n n C4' C5' TPP sing 404 n y N4' HN41 TPP sing 405 n n N4' HN42 TPP sing 406 n n C5' C6' TPP doub 407 n y C5' C7' TPP sing 408 n n C6' H6' TPP sing 409 n n C7' N3 TPP sing 410 n n C7' "H7'1" TPP sing 411 n n C7' "H7'2" TPP sing 412 n n N3 C2 TPP doub 413 n y N3 C4 TPP sing 414 n y C2 S1 TPP sing 415 n y C2 H2 TPP sing 416 n n S1 C5 TPP sing 417 n y C5 C4 TPP doub 418 n y C5 C6 TPP sing 419 n n C4 CM4 TPP sing 420 n n CM4 HM41 TPP sing 421 n n CM4 HM42 TPP sing 422 n n CM4 HM43 TPP sing 423 n n C6 C7 TPP sing 424 n n C6 H61 TPP sing 425 n n C6 H62 TPP sing 426 n n C7 O7 TPP sing 427 n n C7 H71 TPP sing 428 n n C7 H72 TPP sing 429 n n O7 PA TPP sing 430 n n PA O1A TPP doub 431 n n PA O2A TPP sing 432 n n PA O3A TPP sing 433 n n O2A HOA2 TPP sing 434 n n O3A PB TPP sing 435 n n PB O1B TPP doub 436 n n PB O2B TPP sing 437 n n PB O3B TPP sing 438 n n O2B HOB2 TPP sing 439 n n O3B HOB3 TPP sing 440 n n # _atom_sites.entry_id 8P5T _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 G 2 MG A 1 1301 3 MG MG . H 3 ACO A 1 1302 1401 ACO ACO . I 4 TPP A 1 1303 1501 TPP TPP . J 2 MG B 1 1301 6 MG MG . K 3 ACO B 1 1302 1401 ACO ACO . L 4 TPP B 1 1303 1501 TPP TPP . M 2 MG C 1 1301 2 MG MG . N 3 ACO C 1 1302 1401 ACO ACO . O 4 TPP C 1 1303 1501 TPP TPP . P 2 MG D 1 1301 4 MG MG . Q 3 ACO D 1 1302 1401 ACO ACO . R 4 TPP D 1 1303 1501 TPP TPP . S 2 MG E 1 1301 1 MG MG . T 3 ACO E 1 1302 1401 ACO ACO . U 4 TPP E 1 1303 1501 TPP TPP . V 2 MG F 1 1301 5 MG MG . W 3 ACO F 1 1302 1401 ACO ACO . X 4 TPP F 1 1303 1501 TPP TPP . # 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 . . . I 4 168.362 94.045 154.166 1 46.83 ? N1' TPP 1303 A 1 HETATM 2 C C2' TPP . . . I 4 169.458 93.846 154.892 1 44.49 ? C2' TPP 1303 A 1 HETATM 3 C CM2 TPP . . . I 4 169.322 93.903 156.377 1 47.88 ? CM2 TPP 1303 A 1 HETATM 4 N N3' TPP . . . I 4 170.666 93.602 154.39 1 47.36 ? N3' TPP 1303 A 1 HETATM 5 C C4' TPP . . . I 4 170.79 93.548 153.059 1 43.39 ? C4' TPP 1303 A 1 HETATM 6 N N4' TPP . . . I 4 172.019 93.292 152.592 1 47.64 ? N4' TPP 1303 A 1 HETATM 7 C C5' TPP . . . I 4 169.693 93.754 152.207 1 42.17 ? C5' TPP 1303 A 1 HETATM 8 C C6' TPP . . . I 4 168.492 93.992 152.837 1 45.4 ? C6' TPP 1303 A 1 HETATM 9 C C7' TPP . . . I 4 169.786 93.713 150.696 1 41.68 ? C7' TPP 1303 A 1 HETATM 10 N N3 TPP . . . I 4 170.506 94.851 150.121 1 39.48 ? N3 TPP 1303 A 1 HETATM 11 C C2 TPP . . . I 4 171.811 94.801 149.762 1 38.22 ? C2 TPP 1303 A 1 HETATM 12 S S1 TPP . . . I 4 172.284 96.258 149.17 1 34.12 ? S1 TPP 1303 A 1 HETATM 13 C C5 TPP . . . I 4 170.848 97.007 149.309 1 32.18 ? C5 TPP 1303 A 1 HETATM 14 C C4 TPP . . . I 4 169.948 96.106 149.853 1 38.61 ? C4 TPP 1303 A 1 HETATM 15 C CM4 TPP . . . I 4 168.512 96.396 150.166 1 46.67 ? CM4 TPP 1303 A 1 HETATM 16 C C6 TPP . . . I 4 170.771 98.422 148.87 1 30.71 ? C6 TPP 1303 A 1 HETATM 17 C C7 TPP . . . I 4 171.514 99.306 149.799 1 30.07 ? C7 TPP 1303 A 1 HETATM 18 O O7 TPP . . . I 4 171.336 100.676 149.39 1 29.11 ? O7 TPP 1303 A 1 HETATM 19 P PA TPP . . . I 4 172.313 101.789 149.979 1 21.18 ? PA TPP 1303 A 1 HETATM 20 O O1A TPP . . . I 4 171.986 103.087 149.342 1 31.93 ? O1A TPP 1303 A 1 HETATM 21 O O2A TPP . . . I 4 172.301 101.713 151.454 1 30.69 ? O2A TPP 1303 A 1 HETATM 22 O O3A TPP . . . I 4 173.707 101.296 149.386 1 28.18 ? O3A TPP 1303 A 1 HETATM 23 P PB TPP . . . I 4 174.59 101.683 148.108 1 19.75 ? PB TPP 1303 A 1 HETATM 24 O O1B TPP . . . I 4 174.394 100.591 147.149 1 28.43 ? O1B TPP 1303 A 1 HETATM 25 O O2B TPP . . . I 4 174.018 102.964 147.666 1 28.76 ? O2B TPP 1303 A 1 HETATM 26 O O3B TPP . . . I 4 175.99 101.798 148.557 1 29.65 ? O3B TPP 1303 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 76 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 26 #