data_6KM9 # _model_server_result.job_id SqoXYCdb6G7CbCAE_qn0tA _model_server_result.datetime_utc '2024-11-28 16:59:13' _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 6km9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1003}' # _entry.id 6KM9 # _exptl.entry_id 6KM9 _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 100.56 _cell.angle_gamma 90 _cell.entry_id 6KM9 _cell.length_a 84.271 _cell.length_b 76.708 _cell.length_c 144.579 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 E N N ? 4 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 305 A ASP 360 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc2 A OD1 ASN 338 A ASN 393 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc3 A O VAL 340 A VAL 395 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc4 A OE1 GLU 610 A GLU 665 1_555 F CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc5 D MG MG . A MG 1002 1_555 E O1A TPP . A TPP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc6 D MG MG . A MG 1002 1_555 E O1B TPP . A TPP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc7 D MG MG . A MG 1002 1_555 J O HOH . A HOH 1121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc8 F CA CA . A CA 1004 1_555 B OE1 GLU 610 B GLU 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc9 B OD1 ASP 305 B ASP 360 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc10 B OD1 ASN 338 B ASN 393 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc11 B O VAL 340 B VAL 395 1_555 H MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc12 H MG MG . B MG 1002 1_555 I O1A TPP . B TPP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc13 H MG MG . B MG 1002 1_555 I O3B TPP . B TPP 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? # _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 350 n y N1' C6' TPP sing 351 n y C2' CM2 TPP sing 352 n n C2' N3' TPP sing 353 n y CM2 HM21 TPP sing 354 n n CM2 HM22 TPP sing 355 n n CM2 HM23 TPP sing 356 n n N3' C4' TPP doub 357 n y C4' N4' TPP sing 358 n n C4' C5' TPP sing 359 n y N4' HN41 TPP sing 360 n n N4' HN42 TPP sing 361 n n C5' C6' TPP doub 362 n y C5' C7' TPP sing 363 n n C6' H6' TPP sing 364 n n C7' N3 TPP sing 365 n n C7' "H7'1" TPP sing 366 n n C7' "H7'2" TPP sing 367 n n N3 C2 TPP doub 368 n y N3 C4 TPP sing 369 n y C2 S1 TPP sing 370 n y C2 H2 TPP sing 371 n n S1 C5 TPP sing 372 n y C5 C4 TPP doub 373 n y C5 C6 TPP sing 374 n n C4 CM4 TPP sing 375 n n CM4 HM41 TPP sing 376 n n CM4 HM42 TPP sing 377 n n CM4 HM43 TPP sing 378 n n C6 C7 TPP sing 379 n n C6 H61 TPP sing 380 n n C6 H62 TPP sing 381 n n C7 O7 TPP sing 382 n n C7 H71 TPP sing 383 n n C7 H72 TPP sing 384 n n O7 PA TPP sing 385 n n PA O1A TPP doub 386 n n PA O2A TPP sing 387 n n PA O3A TPP sing 388 n n O2A HOA2 TPP sing 389 n n O3A PB TPP sing 390 n n PB O1B TPP doub 391 n n PB O2B TPP sing 392 n n PB O3B TPP sing 393 n n O2B HOB2 TPP sing 394 n n O3B HOB3 TPP sing 395 n n # _atom_sites.entry_id 6KM9 _atom_sites.fract_transf_matrix[1][1] 0.011866 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002211 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013036 _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] 0.007036 _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 P6G A 1 1001 999 P6G P6G . D 3 MG A 1 1002 1000 MG MG . E 4 TPP A 1 1003 1001 TPP TPP . F 5 CA A 1 1004 1000 CA CA . G 2 P6G B 1 1001 999 P6G P6G . H 3 MG B 1 1002 1000 MG MG . I 4 TPP B 1 1003 1001 TPP TPP . J 6 HOH A 1 1101 36 HOH HOH . J 6 HOH A 2 1102 6 HOH HOH . J 6 HOH A 3 1103 91 HOH HOH . J 6 HOH A 4 1104 15 HOH HOH . J 6 HOH A 5 1105 71 HOH HOH . J 6 HOH A 6 1106 133 HOH HOH . J 6 HOH A 7 1107 138 HOH HOH . J 6 HOH A 8 1108 101 HOH HOH . J 6 HOH A 9 1109 34 HOH HOH . J 6 HOH A 10 1110 130 HOH HOH . J 6 HOH A 11 1111 12 HOH HOH . J 6 HOH A 12 1112 114 HOH HOH . J 6 HOH A 13 1113 32 HOH HOH . J 6 HOH A 14 1114 105 HOH HOH . J 6 HOH A 15 1115 49 HOH HOH . J 6 HOH A 16 1116 7 HOH HOH . J 6 HOH A 17 1117 61 HOH HOH . J 6 HOH A 18 1118 65 HOH HOH . J 6 HOH A 19 1119 41 HOH HOH . J 6 HOH A 20 1120 35 HOH HOH . J 6 HOH A 21 1121 5 HOH HOH . J 6 HOH A 22 1122 66 HOH HOH . J 6 HOH A 23 1123 8 HOH HOH . J 6 HOH A 24 1124 92 HOH HOH . J 6 HOH A 25 1125 17 HOH HOH . J 6 HOH A 26 1126 62 HOH HOH . J 6 HOH A 27 1127 119 HOH HOH . J 6 HOH A 28 1128 106 HOH HOH . J 6 HOH A 29 1129 53 HOH HOH . J 6 HOH A 30 1130 28 HOH HOH . J 6 HOH A 31 1131 129 HOH HOH . J 6 HOH A 32 1132 90 HOH HOH . J 6 HOH A 33 1133 77 HOH HOH . J 6 HOH A 34 1134 59 HOH HOH . J 6 HOH A 35 1135 37 HOH HOH . J 6 HOH A 36 1136 82 HOH HOH . J 6 HOH A 37 1137 40 HOH HOH . J 6 HOH A 38 1138 103 HOH HOH . J 6 HOH A 39 1139 104 HOH HOH . J 6 HOH A 40 1140 113 HOH HOH . J 6 HOH A 41 1141 117 HOH HOH . J 6 HOH A 42 1142 88 HOH HOH . J 6 HOH A 43 1143 107 HOH HOH . J 6 HOH A 44 1144 86 HOH HOH . J 6 HOH A 45 1145 80 HOH HOH . J 6 HOH A 46 1146 33 HOH HOH . J 6 HOH A 47 1147 75 HOH HOH . J 6 HOH A 48 1148 94 HOH HOH . J 6 HOH A 49 1149 31 HOH HOH . J 6 HOH A 50 1150 47 HOH HOH . J 6 HOH A 51 1151 19 HOH HOH . J 6 HOH A 52 1152 134 HOH HOH . J 6 HOH A 53 1153 124 HOH HOH . J 6 HOH A 54 1154 27 HOH HOH . J 6 HOH A 55 1155 72 HOH HOH . J 6 HOH A 56 1156 128 HOH HOH . J 6 HOH A 57 1157 38 HOH HOH . J 6 HOH A 58 1158 51 HOH HOH . J 6 HOH A 59 1159 57 HOH HOH . J 6 HOH A 60 1160 56 HOH HOH . J 6 HOH A 61 1161 121 HOH HOH . J 6 HOH A 62 1162 89 HOH HOH . J 6 HOH A 63 1163 97 HOH HOH . J 6 HOH A 64 1164 137 HOH HOH . J 6 HOH A 65 1165 116 HOH HOH . J 6 HOH A 66 1166 122 HOH HOH . J 6 HOH A 67 1167 93 HOH HOH . J 6 HOH A 68 1168 111 HOH HOH . J 6 HOH A 69 1169 139 HOH HOH . J 6 HOH A 70 1170 87 HOH HOH . K 6 HOH B 1 1101 102 HOH HOH . K 6 HOH B 2 1102 112 HOH HOH . K 6 HOH B 3 1103 125 HOH HOH . K 6 HOH B 4 1104 109 HOH HOH . K 6 HOH B 5 1105 13 HOH HOH . K 6 HOH B 6 1106 132 HOH HOH . K 6 HOH B 7 1107 26 HOH HOH . K 6 HOH B 8 1108 98 HOH HOH . K 6 HOH B 9 1109 3 HOH HOH . K 6 HOH B 10 1110 73 HOH HOH . K 6 HOH B 11 1111 74 HOH HOH . K 6 HOH B 12 1112 58 HOH HOH . K 6 HOH B 13 1113 100 HOH HOH . K 6 HOH B 14 1114 55 HOH HOH . K 6 HOH B 15 1115 4 HOH HOH . K 6 HOH B 16 1116 69 HOH HOH . K 6 HOH B 17 1117 123 HOH HOH . K 6 HOH B 18 1118 81 HOH HOH . K 6 HOH B 19 1119 25 HOH HOH . K 6 HOH B 20 1120 30 HOH HOH . K 6 HOH B 21 1121 70 HOH HOH . K 6 HOH B 22 1122 2 HOH HOH . K 6 HOH B 23 1123 29 HOH HOH . K 6 HOH B 24 1124 68 HOH HOH . K 6 HOH B 25 1125 10 HOH HOH . K 6 HOH B 26 1126 24 HOH HOH . K 6 HOH B 27 1127 108 HOH HOH . K 6 HOH B 28 1128 48 HOH HOH . K 6 HOH B 29 1129 14 HOH HOH . K 6 HOH B 30 1130 43 HOH HOH . K 6 HOH B 31 1131 44 HOH HOH . K 6 HOH B 32 1132 45 HOH HOH . K 6 HOH B 33 1133 110 HOH HOH . K 6 HOH B 34 1134 9 HOH HOH . K 6 HOH B 35 1135 42 HOH HOH . K 6 HOH B 36 1136 78 HOH HOH . K 6 HOH B 37 1137 84 HOH HOH . K 6 HOH B 38 1138 39 HOH HOH . K 6 HOH B 39 1139 118 HOH HOH . K 6 HOH B 40 1140 1 HOH HOH . K 6 HOH B 41 1141 52 HOH HOH . K 6 HOH B 42 1142 11 HOH HOH . K 6 HOH B 43 1143 22 HOH HOH . K 6 HOH B 44 1144 60 HOH HOH . K 6 HOH B 45 1145 95 HOH HOH . K 6 HOH B 46 1146 64 HOH HOH . K 6 HOH B 47 1147 131 HOH HOH . K 6 HOH B 48 1148 16 HOH HOH . K 6 HOH B 49 1149 21 HOH HOH . K 6 HOH B 50 1150 20 HOH HOH . K 6 HOH B 51 1151 76 HOH HOH . K 6 HOH B 52 1152 120 HOH HOH . K 6 HOH B 53 1153 63 HOH HOH . K 6 HOH B 54 1154 23 HOH HOH . K 6 HOH B 55 1155 79 HOH HOH . K 6 HOH B 56 1156 46 HOH HOH . K 6 HOH B 57 1157 135 HOH HOH . K 6 HOH B 58 1158 54 HOH HOH . K 6 HOH B 59 1159 83 HOH HOH . K 6 HOH B 60 1160 18 HOH HOH . K 6 HOH B 61 1161 136 HOH HOH . K 6 HOH B 62 1162 85 HOH HOH . K 6 HOH B 63 1163 67 HOH HOH . K 6 HOH B 64 1164 96 HOH HOH . K 6 HOH B 65 1165 99 HOH HOH . K 6 HOH B 66 1166 50 HOH HOH . K 6 HOH B 67 1167 127 HOH HOH . K 6 HOH B 68 1168 126 HOH HOH . K 6 HOH B 69 1169 115 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 . . . E 4 -31.42 8.891 -33.539 1 32.87 ? N1' TPP 1003 A 1 HETATM 2 C C2' TPP . . . E 4 -31.516 7.604 -33.553 1 31.72 ? C2' TPP 1003 A 1 HETATM 3 C CM2 TPP . . . E 4 -30.296 6.688 -33.758 1 31.42 ? CM2 TPP 1003 A 1 HETATM 4 N N3' TPP . . . E 4 -32.84 6.959 -33.369 1 31.48 ? N3' TPP 1003 A 1 HETATM 5 C C4' TPP . . . E 4 -33.873 7.634 -33.194 1 32.03 ? C4' TPP 1003 A 1 HETATM 6 N N4' TPP . . . E 4 -35.122 6.905 -33.035 1 32.48 ? N4' TPP 1003 A 1 HETATM 7 C C5' TPP . . . E 4 -33.786 9.134 -33.175 1 34.45 ? C5' TPP 1003 A 1 HETATM 8 C C6' TPP . . . E 4 -32.633 9.702 -33.34 1 34.73 ? C6' TPP 1003 A 1 HETATM 9 C C7' TPP . . . E 4 -35.053 10.004 -32.976 1 36.48 ? C7' TPP 1003 A 1 HETATM 10 N N3 TPP . . . E 4 -35.93 9.841 -34.139 1 36.93 ? N3 TPP 1003 A 1 HETATM 11 C C2 TPP . . . E 4 -36.956 8.952 -34.194 1 38.95 ? C2 TPP 1003 A 1 HETATM 12 S S1 TPP . . . E 4 -37.724 8.967 -35.56 1 39.24 ? S1 TPP 1003 A 1 HETATM 13 C C5 TPP . . . E 4 -36.843 10.22 -36.439 1 34.52 ? C5 TPP 1003 A 1 HETATM 14 C C4 TPP . . . E 4 -35.726 10.719 -35.481 1 35.3 ? C4 TPP 1003 A 1 HETATM 15 C CM4 TPP . . . E 4 -34.668 11.796 -35.73 1 35.82 ? CM4 TPP 1003 A 1 HETATM 16 C C6 TPP . . . E 4 -37.126 10.692 -37.863 1 30.13 ? C6 TPP 1003 A 1 HETATM 17 C C7 TPP . . . E 4 -37.199 9.425 -38.716 1 27.54 ? C7 TPP 1003 A 1 HETATM 18 O O7 TPP . . . E 4 -37.161 9.856 -40.052 1 27.12 ? O7 TPP 1003 A 1 HETATM 19 P PA TPP . . . E 4 -37.186 8.708 -41.232 1 29.84 ? PA TPP 1003 A 1 HETATM 20 O O1A TPP . . . E 4 -37.431 9.339 -42.536 1 27.84 ? O1A TPP 1003 A 1 HETATM 21 O O2A TPP . . . E 4 -35.954 7.944 -41.39 1 26.43 ? O2A TPP 1003 A 1 HETATM 22 O O3A TPP . . . E 4 -38.274 7.595 -40.804 1 26.61 ? O3A TPP 1003 A 1 HETATM 23 P PB TPP . . . E 4 -39.853 7.897 -40.9 1 33.57 ? PB TPP 1003 A 1 HETATM 24 O O1B TPP . . . E 4 -40.163 9.133 -41.629 1 26.93 ? O1B TPP 1003 A 1 HETATM 25 O O2B TPP . . . E 4 -40.5 6.799 -41.615 1 30.75 ? O2B TPP 1003 A 1 HETATM 26 O O3B TPP . . . E 4 -40.486 7.995 -39.582 1 29.23 ? O3B TPP 1003 A 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 26 #