data_8P5U # _model_server_result.job_id CuuU5TsT6obemOvGaJEpzw _model_server_result.datetime_utc '2024-11-29 19:12:33' _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 8p5u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1304}' # _entry.id 8P5U # _exptl.entry_id 8P5U _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 425.314 _entity.id 5 _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 8P5U _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8P5U _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,Y,Z,AA,BA,CA,DA _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 ? 5 J N N ? 5 N N N ? 5 R N N ? 5 V N N ? 5 Z N N ? 5 DA 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc2 A OD1 ASN 680 A ASN 678 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc3 A O ILE 682 A ILE 680 1_555 G MG MG . A MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc4 G MG MG . A MG 1301 1_555 J O2B TPP . A TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc5 G MG MG . A MG 1301 1_555 J O1A TPP . A TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc6 B OD1 ASP 647 B ASP 645 1_555 K MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc7 B OD1 ASN 680 B ASN 678 1_555 K MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc8 B O ILE 682 B ILE 680 1_555 K MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc9 K MG MG . B MG 1301 1_555 N O2A TPP . B TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc10 K MG MG . B MG 1301 1_555 N O2B TPP . B TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc11 C OD1 ASP 647 C ASP 645 1_555 O MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc12 C OD1 ASN 680 C ASN 678 1_555 O MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc13 C O ILE 682 C ILE 680 1_555 O MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc14 O MG MG . C MG 1301 1_555 R O2B TPP . C TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc15 O MG MG . C MG 1301 1_555 R O1A TPP . C TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc16 D OD1 ASP 647 D ASP 645 1_555 S MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc17 D OD1 ASN 680 D ASN 678 1_555 S MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc18 D O ILE 682 D ILE 680 1_555 S MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc19 S MG MG . D MG 1301 1_555 V O2A TPP . D TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc20 S MG MG . D MG 1301 1_555 V O2B TPP . D TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc21 E OD1 ASP 647 E ASP 645 1_555 W MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc22 E OD1 ASN 680 E ASN 678 1_555 W MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc23 E O ILE 682 E ILE 680 1_555 W MG MG . E MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc24 W MG MG . E MG 1301 1_555 Z O2B TPP . E TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc25 W MG MG . E MG 1301 1_555 Z O1A TPP . E TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc26 F OD1 ASP 647 F ASP 645 1_555 AA MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc27 F OD1 ASN 680 F ASN 678 1_555 AA MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc28 F O ILE 682 F ILE 680 1_555 AA MG MG . F MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc29 AA MG MG . F MG 1301 1_555 DA O2B TPP . F TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc30 AA MG MG . F MG 1301 1_555 DA O2A TPP . F TPP 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? # _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 481 n y N1' C6' TPP sing 482 n y C2' CM2 TPP sing 483 n n C2' N3' TPP sing 484 n y CM2 HM21 TPP sing 485 n n CM2 HM22 TPP sing 486 n n CM2 HM23 TPP sing 487 n n N3' C4' TPP doub 488 n y C4' N4' TPP sing 489 n n C4' C5' TPP sing 490 n y N4' HN41 TPP sing 491 n n N4' HN42 TPP sing 492 n n C5' C6' TPP doub 493 n y C5' C7' TPP sing 494 n n C6' H6' TPP sing 495 n n C7' N3 TPP sing 496 n n C7' "H7'1" TPP sing 497 n n C7' "H7'2" TPP sing 498 n n N3 C2 TPP doub 499 n y N3 C4 TPP sing 500 n y C2 S1 TPP sing 501 n y C2 H2 TPP sing 502 n n S1 C5 TPP sing 503 n y C5 C4 TPP doub 504 n y C5 C6 TPP sing 505 n n C4 CM4 TPP sing 506 n n CM4 HM41 TPP sing 507 n n CM4 HM42 TPP sing 508 n n CM4 HM43 TPP sing 509 n n C6 C7 TPP sing 510 n n C6 H61 TPP sing 511 n n C6 H62 TPP sing 512 n n C7 O7 TPP sing 513 n n C7 H71 TPP sing 514 n n C7 H72 TPP sing 515 n n O7 PA TPP sing 516 n n PA O1A TPP doub 517 n n PA O2A TPP sing 518 n n PA O3A TPP sing 519 n n O2A HOA2 TPP sing 520 n n O3A PB TPP sing 521 n n PB O1B TPP doub 522 n n PB O2B TPP sing 523 n n PB O3B TPP sing 524 n n O2B HOB2 TPP sing 525 n n O3B HOB3 TPP sing 526 n n # _atom_sites.entry_id 8P5U _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 COA A 1 1302 1304 COA COA . I 4 ACO A 1 1303 1401 ACO ACO . J 5 TPP A 1 1304 1501 TPP TPP . K 2 MG B 1 1301 6 MG MG . L 3 COA B 1 1302 1304 COA COA . M 4 ACO B 1 1303 1401 ACO ACO . N 5 TPP B 1 1304 1501 TPP TPP . O 2 MG C 1 1301 2 MG MG . P 3 COA C 1 1302 1304 COA COA . Q 4 ACO C 1 1303 1401 ACO ACO . R 5 TPP C 1 1304 1501 TPP TPP . S 2 MG D 1 1301 4 MG MG . T 3 COA D 1 1302 1304 COA COA . U 4 ACO D 1 1303 1401 ACO ACO . V 5 TPP D 1 1304 1501 TPP TPP . W 2 MG E 1 1301 1 MG MG . X 3 COA E 1 1302 1304 COA COA . Y 4 ACO E 1 1303 1401 ACO ACO . Z 5 TPP E 1 1304 1501 TPP TPP . AA 2 MG F 1 1301 5 MG MG . BA 3 COA F 1 1302 1304 COA COA . CA 4 ACO F 1 1303 1401 ACO ACO . DA 5 TPP F 1 1304 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 . . . N 5 161.991 94.101 175.207 1 46.69 ? N1' TPP 1304 B 1 HETATM 2 C C2' TPP . . . N 5 160.877 93.927 174.494 1 44.25 ? C2' TPP 1304 B 1 HETATM 3 C CM2 TPP . . . N 5 160.991 94.029 173.009 1 48.27 ? CM2 TPP 1304 B 1 HETATM 4 N N3' TPP . . . N 5 159.663 93.706 174.998 1 47.06 ? N3' TPP 1304 B 1 HETATM 5 C C4' TPP . . . N 5 159.536 93.651 176.331 1 42.53 ? C4' TPP 1304 B 1 HETATM 6 N N4' TPP . . . N 5 158.334 93.324 176.803 1 46.76 ? N4' TPP 1304 B 1 HETATM 7 C C5' TPP . . . N 5 160.661 93.836 177.18 1 41.56 ? C5' TPP 1304 B 1 HETATM 8 C C6' TPP . . . N 5 161.852 94.049 176.534 1 44.69 ? C6' TPP 1304 B 1 HETATM 9 C C7' TPP . . . N 5 160.587 93.817 178.686 1 41.4 ? C7' TPP 1304 B 1 HETATM 10 N N3 TPP . . . N 5 159.814 94.949 179.267 1 39.27 ? N3 TPP 1304 B 1 HETATM 11 C C2 TPP . . . N 5 158.545 94.864 179.594 1 38.44 ? C2 TPP 1304 B 1 HETATM 12 S S1 TPP . . . N 5 157.956 96.299 180.216 1 35.91 ? S1 TPP 1304 B 1 HETATM 13 C C5 TPP . . . N 5 159.445 97.033 180.042 1 32.13 ? C5 TPP 1304 B 1 HETATM 14 C C4 TPP . . . N 5 160.371 96.199 179.518 1 38.95 ? C4 TPP 1304 B 1 HETATM 15 C CM4 TPP . . . N 5 161.801 96.482 179.211 1 46.9 ? CM4 TPP 1304 B 1 HETATM 16 C C6 TPP . . . N 5 159.588 98.475 180.428 1 30.16 ? C6 TPP 1304 B 1 HETATM 17 C C7 TPP . . . N 5 158.754 99.39 179.57 1 29.62 ? C7 TPP 1304 B 1 HETATM 18 O O7 TPP . . . N 5 158.951 100.754 179.998 1 28.56 ? O7 TPP 1304 B 1 HETATM 19 P PA TPP . . . N 5 157.999 101.885 179.428 1 21.68 ? PA TPP 1304 B 1 HETATM 20 O O1A TPP . . . N 5 158.004 101.791 177.964 1 31.36 ? O1A TPP 1304 B 1 HETATM 21 O O2A TPP . . . N 5 158.312 103.183 180.049 1 32.32 ? O2A TPP 1304 B 1 HETATM 22 O O3A TPP . . . N 5 156.602 101.402 180.028 1 27.96 ? O3A TPP 1304 B 1 HETATM 23 P PB TPP . . . N 5 155.726 101.779 181.295 1 19.34 ? PB TPP 1304 B 1 HETATM 24 O O1B TPP . . . N 5 154.307 101.871 180.805 1 29.9 ? O1B TPP 1304 B 1 HETATM 25 O O2B TPP . . . N 5 156.297 103.103 181.726 1 27.94 ? O2B TPP 1304 B 1 HETATM 26 O O3B TPP . . . N 5 155.921 100.683 182.304 1 28.3 ? O3B TPP 1304 B 1 # _model_server_stats.io_time_ms 98 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 264 _model_server_stats.query_time_ms 395 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 26 #