data_9DTV # _model_server_result.job_id BkfYBA0JTzWeF4fghKS6Iw _model_server_result.datetime_utc '2025-07-16 10:14:17' _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 9dtv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":601}' # _entry.id 9DTV # _exptl.entry_id 9DTV _exptl.method 'X-RAY DIFFRACTION' # _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 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 90 _cell.entry_id 9DTV _cell.length_a 101.425 _cell.length_b 140.443 _cell.length_c 184.141 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DTV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,O,P,Q,R,S,T,U,V _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 x,y,z _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 G N N ? 4 O 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 B OD1 ASP 460 D ASP 440 1_555 J MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc2 B OD1 ASP 489 D ASP 469 1_555 J MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc3 B O GLY 491 D GLY 471 1_555 J MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc4 G O2A TPP . D TPP 601 1_555 J MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc5 G O1B TPP . D TPP 601 1_555 J MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc6 J MG MG . D MG 604 1_555 T O HOH . D HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc7 D OD1 ASP 460 C ASP 440 1_555 Q MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc8 D OD1 ASP 489 C ASP 469 1_555 Q MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc9 D O GLY 491 C GLY 471 1_555 Q MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc10 O O2A TPP . C TPP 601 1_555 Q MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc11 O O3B TPP . C TPP 601 1_555 Q MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc12 Q MG MG . C MG 603 1_555 V O HOH . C HOH 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? # _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 352 n y N1' C6' TPP sing 353 n y C2' CM2 TPP sing 354 n n C2' N3' TPP sing 355 n y CM2 HM21 TPP sing 356 n n CM2 HM22 TPP sing 357 n n CM2 HM23 TPP sing 358 n n N3' C4' TPP doub 359 n y C4' N4' TPP sing 360 n n C4' C5' TPP sing 361 n y N4' HN41 TPP sing 362 n n N4' HN42 TPP sing 363 n n C5' C6' TPP doub 364 n y C5' C7' TPP sing 365 n n C6' H6' TPP sing 366 n n C7' N3 TPP sing 367 n n C7' "H7'1" TPP sing 368 n n C7' "H7'2" TPP sing 369 n n N3 C2 TPP doub 370 n y N3 C4 TPP sing 371 n y C2 S1 TPP sing 372 n y C2 H2 TPP sing 373 n n S1 C5 TPP sing 374 n y C5 C4 TPP doub 375 n y C5 C6 TPP sing 376 n n C4 CM4 TPP sing 377 n n CM4 HM41 TPP sing 378 n n CM4 HM42 TPP sing 379 n n CM4 HM43 TPP sing 380 n n C6 C7 TPP sing 381 n n C6 H61 TPP sing 382 n n C6 H62 TPP sing 383 n n C7 O7 TPP sing 384 n n C7 H71 TPP sing 385 n n C7 H72 TPP sing 386 n n O7 PA TPP sing 387 n n PA O1A TPP doub 388 n n PA O2A TPP sing 389 n n PA O3A TPP sing 390 n n O2A HOA2 TPP sing 391 n n O3A PB TPP sing 392 n n PB O1B TPP doub 393 n n PB O2B TPP sing 394 n n PB O3B TPP sing 395 n n O2B HOB2 TPP sing 396 n n O3B HOB3 TPP sing 397 n n # _atom_sites.entry_id 9DTV _atom_sites.fract_transf_matrix[1][1] 0.00986 _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] 0.00712 _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] 0.005431 _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 E 2 GOL A 1 601 601 GOL GOL . F 3 CL A 1 602 2 CL CL . G 4 TPP D 1 601 601 TPP TPP . H 5 DNA D 1 602 602 DNA DNA . I 6 EDO D 1 603 603 EDO EDO . J 7 MG D 1 604 1 MG MG . K 3 CL D 1 605 1 CL CL . L 3 CL D 1 606 5 CL CL . M 2 GOL B 1 601 602 GOL GOL . N 3 CL B 1 602 3 CL CL . O 4 TPP C 1 601 601 TPP TPP . P 5 DNA C 1 602 602 DNA DNA . Q 7 MG C 1 603 2 MG MG . R 3 CL C 1 604 4 CL CL . S 8 HOH A 1 701 3 HOH HOH . S 8 HOH A 2 702 15 HOH HOH . S 8 HOH A 3 703 7 HOH HOH . S 8 HOH A 4 704 4 HOH HOH . S 8 HOH A 5 705 126 HOH HOH . S 8 HOH A 6 706 46 HOH HOH . S 8 HOH A 7 707 37 HOH HOH . S 8 HOH A 8 708 119 HOH HOH . S 8 HOH A 9 709 125 HOH HOH . S 8 HOH A 10 710 96 HOH HOH . S 8 HOH A 11 711 5 HOH HOH . S 8 HOH A 12 712 84 HOH HOH . S 8 HOH A 13 713 10 HOH HOH . S 8 HOH A 14 714 11 HOH HOH . S 8 HOH A 15 715 12 HOH HOH . S 8 HOH A 16 716 42 HOH HOH . S 8 HOH A 17 717 56 HOH HOH . S 8 HOH A 18 718 118 HOH HOH . S 8 HOH A 19 719 40 HOH HOH . S 8 HOH A 20 720 13 HOH HOH . S 8 HOH A 21 721 82 HOH HOH . S 8 HOH A 22 722 152 HOH HOH . S 8 HOH A 23 723 52 HOH HOH . S 8 HOH A 24 724 28 HOH HOH . S 8 HOH A 25 725 69 HOH HOH . S 8 HOH A 26 726 83 HOH HOH . S 8 HOH A 27 727 57 HOH HOH . S 8 HOH A 28 728 124 HOH HOH . S 8 HOH A 29 729 8 HOH HOH . S 8 HOH A 30 730 6 HOH HOH . S 8 HOH A 31 731 54 HOH HOH . S 8 HOH A 32 732 2 HOH HOH . S 8 HOH A 33 733 76 HOH HOH . S 8 HOH A 34 734 89 HOH HOH . S 8 HOH A 35 735 148 HOH HOH . S 8 HOH A 36 736 127 HOH HOH . S 8 HOH A 37 737 149 HOH HOH . S 8 HOH A 38 738 122 HOH HOH . T 8 HOH D 1 701 99 HOH HOH . T 8 HOH D 2 702 39 HOH HOH . T 8 HOH D 3 703 48 HOH HOH . T 8 HOH D 4 704 23 HOH HOH . T 8 HOH D 5 705 128 HOH HOH . T 8 HOH D 6 706 1 HOH HOH . T 8 HOH D 7 707 101 HOH HOH . T 8 HOH D 8 708 130 HOH HOH . T 8 HOH D 9 709 90 HOH HOH . T 8 HOH D 10 710 19 HOH HOH . T 8 HOH D 11 711 25 HOH HOH . T 8 HOH D 12 712 24 HOH HOH . T 8 HOH D 13 713 131 HOH HOH . T 8 HOH D 14 714 104 HOH HOH . T 8 HOH D 15 715 117 HOH HOH . T 8 HOH D 16 716 80 HOH HOH . T 8 HOH D 17 717 85 HOH HOH . T 8 HOH D 18 718 26 HOH HOH . T 8 HOH D 19 719 16 HOH HOH . T 8 HOH D 20 720 62 HOH HOH . T 8 HOH D 21 721 67 HOH HOH . T 8 HOH D 22 722 64 HOH HOH . T 8 HOH D 23 723 120 HOH HOH . T 8 HOH D 24 724 91 HOH HOH . T 8 HOH D 25 725 43 HOH HOH . T 8 HOH D 26 726 140 HOH HOH . T 8 HOH D 27 727 22 HOH HOH . T 8 HOH D 28 728 81 HOH HOH . T 8 HOH D 29 729 113 HOH HOH . T 8 HOH D 30 730 18 HOH HOH . T 8 HOH D 31 731 41 HOH HOH . T 8 HOH D 32 732 21 HOH HOH . T 8 HOH D 33 733 58 HOH HOH . T 8 HOH D 34 734 20 HOH HOH . T 8 HOH D 35 735 53 HOH HOH . T 8 HOH D 36 736 17 HOH HOH . T 8 HOH D 37 737 115 HOH HOH . T 8 HOH D 38 738 27 HOH HOH . T 8 HOH D 39 739 114 HOH HOH . T 8 HOH D 40 740 129 HOH HOH . T 8 HOH D 41 741 106 HOH HOH . T 8 HOH D 42 742 108 HOH HOH . T 8 HOH D 43 743 55 HOH HOH . T 8 HOH D 44 744 103 HOH HOH . T 8 HOH D 45 745 109 HOH HOH . T 8 HOH D 46 746 61 HOH HOH . T 8 HOH D 47 747 29 HOH HOH . T 8 HOH D 48 748 110 HOH HOH . T 8 HOH D 49 749 121 HOH HOH . T 8 HOH D 50 750 133 HOH HOH . T 8 HOH D 51 751 132 HOH HOH . T 8 HOH D 52 752 123 HOH HOH . U 8 HOH B 1 701 92 HOH HOH . U 8 HOH B 2 702 137 HOH HOH . U 8 HOH B 3 703 38 HOH HOH . U 8 HOH B 4 704 75 HOH HOH . U 8 HOH B 5 705 105 HOH HOH . U 8 HOH B 6 706 59 HOH HOH . U 8 HOH B 7 707 134 HOH HOH . U 8 HOH B 8 708 70 HOH HOH . U 8 HOH B 9 709 153 HOH HOH . U 8 HOH B 10 710 72 HOH HOH . U 8 HOH B 11 711 139 HOH HOH . U 8 HOH B 12 712 79 HOH HOH . U 8 HOH B 13 713 51 HOH HOH . U 8 HOH B 14 714 33 HOH HOH . U 8 HOH B 15 715 93 HOH HOH . U 8 HOH B 16 716 74 HOH HOH . U 8 HOH B 17 717 102 HOH HOH . U 8 HOH B 18 718 50 HOH HOH . U 8 HOH B 19 719 44 HOH HOH . U 8 HOH B 20 720 45 HOH HOH . U 8 HOH B 21 721 60 HOH HOH . U 8 HOH B 22 722 63 HOH HOH . U 8 HOH B 23 723 30 HOH HOH . U 8 HOH B 24 724 31 HOH HOH . U 8 HOH B 25 725 95 HOH HOH . U 8 HOH B 26 726 32 HOH HOH . U 8 HOH B 27 727 49 HOH HOH . U 8 HOH B 28 728 98 HOH HOH . U 8 HOH B 29 729 116 HOH HOH . U 8 HOH B 30 730 138 HOH HOH . U 8 HOH B 31 731 146 HOH HOH . U 8 HOH B 32 732 135 HOH HOH . V 8 HOH C 1 701 78 HOH HOH . V 8 HOH C 2 702 77 HOH HOH . V 8 HOH C 3 703 145 HOH HOH . V 8 HOH C 4 704 71 HOH HOH . V 8 HOH C 5 705 35 HOH HOH . V 8 HOH C 6 706 112 HOH HOH . V 8 HOH C 7 707 141 HOH HOH . V 8 HOH C 8 708 36 HOH HOH . V 8 HOH C 9 709 144 HOH HOH . V 8 HOH C 10 710 111 HOH HOH . V 8 HOH C 11 711 47 HOH HOH . V 8 HOH C 12 712 100 HOH HOH . V 8 HOH C 13 713 154 HOH HOH . V 8 HOH C 14 714 34 HOH HOH . V 8 HOH C 15 715 147 HOH HOH . V 8 HOH C 16 716 143 HOH HOH . V 8 HOH C 17 717 142 HOH HOH . V 8 HOH C 18 718 150 HOH HOH . V 8 HOH C 19 719 9 HOH HOH . V 8 HOH C 20 720 151 HOH HOH . V 8 HOH C 21 721 136 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 . . . G 4 32.17 6.293 16.699 1 58.01 ? N1' TPP 601 D 1 HETATM 2 C C2' TPP . . . G 4 32.318 5.372 17.665 1 51.8 ? C2' TPP 601 D 1 HETATM 3 C CM2 TPP . . . G 4 32.514 3.955 17.233 1 46.14 ? CM2 TPP 601 D 1 HETATM 4 N N3' TPP . . . G 4 32.304 5.614 18.979 1 58.27 ? N3' TPP 601 D 1 HETATM 5 C C4' TPP . . . G 4 32.129 6.885 19.381 1 62.51 ? C4' TPP 601 D 1 HETATM 6 N N4' TPP . . . G 4 32.117 7.111 20.698 1 60.12 ? N4' TPP 601 D 1 HETATM 7 C C5' TPP . . . G 4 31.957 7.937 18.436 1 48.76 ? C5' TPP 601 D 1 HETATM 8 C C6' TPP . . . G 4 31.996 7.553 17.114 1 51.32 ? C6' TPP 601 D 1 HETATM 9 C C7' TPP . . . G 4 31.76 9.378 18.826 1 44.06 ? C7' TPP 601 D 1 HETATM 10 N N3 TPP . . . G 4 30.541 9.612 19.639 1 54.61 ? N3 TPP 601 D 1 HETATM 11 C C2 TPP . . . G 4 30.547 9.732 20.951 1 51.08 ? C2 TPP 601 D 1 HETATM 12 S S1 TPP . . . G 4 29.017 10.001 21.578 1 61.27 ? S1 TPP 601 D 1 HETATM 13 C C5 TPP . . . G 4 28.313 9.955 20.002 1 54.65 ? C5 TPP 601 D 1 HETATM 14 C C4 TPP . . . G 4 29.276 9.742 19.062 1 53.25 ? C4 TPP 601 D 1 HETATM 15 C CM4 TPP . . . G 4 29.098 9.638 17.587 1 37.52 ? CM4 TPP 601 D 1 HETATM 16 C C6 TPP . . . G 4 26.835 10.153 19.808 1 46.12 ? C6 TPP 601 D 1 HETATM 17 C C7 TPP . . . G 4 26.022 8.928 20.158 1 49.59 ? C7 TPP 601 D 1 HETATM 18 O O7 TPP . . . G 4 24.616 9.24 19.998 1 46.58 ? O7 TPP 601 D 1 HETATM 19 P PA TPP . . . G 4 23.452 8.421 20.669 1 51.25 ? PA TPP 601 D 1 HETATM 20 O O1A TPP . . . G 4 23.823 6.991 20.729 1 60.07 ? O1A TPP 601 D 1 HETATM 21 O O2A TPP . . . G 4 22.144 8.734 19.945 1 47.64 ? O2A TPP 601 D 1 HETATM 22 O O3A TPP . . . G 4 23.367 9.058 22.135 1 48.93 ? O3A TPP 601 D 1 HETATM 23 P PB TPP . . . G 4 22.795 10.349 22.861 1 50.13 ? PB TPP 601 D 1 HETATM 24 O O1B TPP . . . G 4 22.032 11.187 21.891 1 51.5 ? O1B TPP 601 D 1 HETATM 25 O O2B TPP . . . G 4 21.936 9.801 24.015 1 50.35 ? O2B TPP 601 D 1 HETATM 26 O O3B TPP . . . G 4 24.034 11.052 23.451 1 48.62 ? O3B TPP 601 D 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 70 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #