data_7QGT # _model_server_result.job_id kdYI3zIknJkKJgBi9ZSYsw _model_server_result.datetime_utc '2024-11-08 19:12:38' _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 7qgt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 7QGT # _exptl.entry_id 7QGT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 7QGT _cell.length_a 125.553 _cell.length_b 134.573 _cell.length_c 169.291 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7QGT _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A NZ LYS 141 A LYS 119 1_555 D C4A PLP . A PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? metalc ? metalc1 A SG CYS 74 A CYS 52 1_555 C FE HEM . A HEM 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc2 A NE2 HIS 87 A HIS 65 1_555 C FE HEM . A HEM 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc3 B SG CYS 74 B CYS 52 1_555 E FE HEM . B HEM 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc4 B NE2 HIS 87 B HIS 65 1_555 E FE HEM . B HEM 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 PLP doub 378 n y N1 C6 PLP sing 379 n y C2 C2A PLP sing 380 n n C2 C3 PLP sing 381 n y C2A H2A1 PLP sing 382 n n C2A H2A2 PLP sing 383 n n C2A H2A3 PLP sing 384 n n C3 O3 PLP sing 385 n n C3 C4 PLP doub 386 n y O3 HO3 PLP sing 387 n n C4 C4A PLP sing 388 n n C4 C5 PLP sing 389 n y C4A O4A PLP doub 390 n n C4A H4A PLP sing 391 n n C5 C6 PLP doub 392 n y C5 C5A PLP sing 393 n n C6 H6 PLP sing 394 n n C5A O4P PLP sing 395 n n C5A H5A1 PLP sing 396 n n C5A H5A2 PLP sing 397 n n O4P P PLP sing 398 n n P O1P PLP doub 399 n n P O2P PLP sing 400 n n P O3P PLP sing 401 n n O2P HOP2 PLP sing 402 n n O3P HOP3 PLP sing 403 n n # _atom_sites.entry_id 7QGT _atom_sites.fract_transf_matrix[1][1] 0.007965 _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] 0.007431 _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] 0.005907 _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 HEM A 1 1000 1000 HEM HEM . D 3 PLP A 1 1001 1001 PLP PLP . E 2 HEM B 1 1000 1000 HEM HEM . F 4 IK2 B 1 1001 1001 IK2 IK2 . G 5 HOH A 1 1101 281 HOH HOH . G 5 HOH A 2 1102 10 HOH HOH . G 5 HOH A 3 1103 131 HOH HOH . G 5 HOH A 4 1104 107 HOH HOH . G 5 HOH A 5 1105 251 HOH HOH . G 5 HOH A 6 1106 148 HOH HOH . G 5 HOH A 7 1107 245 HOH HOH . G 5 HOH A 8 1108 130 HOH HOH . G 5 HOH A 9 1109 230 HOH HOH . G 5 HOH A 10 1110 321 HOH HOH . G 5 HOH A 11 1111 253 HOH HOH . G 5 HOH A 12 1112 29 HOH HOH . G 5 HOH A 13 1113 257 HOH HOH . G 5 HOH A 14 1114 307 HOH HOH . G 5 HOH A 15 1115 80 HOH HOH . G 5 HOH A 16 1116 4 HOH HOH . G 5 HOH A 17 1117 174 HOH HOH . G 5 HOH A 18 1118 238 HOH HOH . G 5 HOH A 19 1119 1 HOH HOH . G 5 HOH A 20 1120 38 HOH HOH . G 5 HOH A 21 1121 109 HOH HOH . G 5 HOH A 22 1122 246 HOH HOH . G 5 HOH A 23 1123 137 HOH HOH . G 5 HOH A 24 1124 96 HOH HOH . G 5 HOH A 25 1125 267 HOH HOH . G 5 HOH A 26 1126 164 HOH HOH . G 5 HOH A 27 1127 43 HOH HOH . G 5 HOH A 28 1128 115 HOH HOH . G 5 HOH A 29 1129 232 HOH HOH . G 5 HOH A 30 1130 151 HOH HOH . G 5 HOH A 31 1131 81 HOH HOH . G 5 HOH A 32 1132 11 HOH HOH . G 5 HOH A 33 1133 72 HOH HOH . G 5 HOH A 34 1134 33 HOH HOH . G 5 HOH A 35 1135 303 HOH HOH . G 5 HOH A 36 1136 71 HOH HOH . G 5 HOH A 37 1137 241 HOH HOH . G 5 HOH A 38 1138 282 HOH HOH . G 5 HOH A 39 1139 122 HOH HOH . G 5 HOH A 40 1140 184 HOH HOH . G 5 HOH A 41 1141 233 HOH HOH . G 5 HOH A 42 1142 22 HOH HOH . G 5 HOH A 43 1143 140 HOH HOH . G 5 HOH A 44 1144 30 HOH HOH . G 5 HOH A 45 1145 177 HOH HOH . G 5 HOH A 46 1146 162 HOH HOH . G 5 HOH A 47 1147 129 HOH HOH . G 5 HOH A 48 1148 242 HOH HOH . G 5 HOH A 49 1149 21 HOH HOH . G 5 HOH A 50 1150 103 HOH HOH . G 5 HOH A 51 1151 42 HOH HOH . G 5 HOH A 52 1152 268 HOH HOH . G 5 HOH A 53 1153 259 HOH HOH . G 5 HOH A 54 1154 16 HOH HOH . G 5 HOH A 55 1155 95 HOH HOH . G 5 HOH A 56 1156 132 HOH HOH . G 5 HOH A 57 1157 64 HOH HOH . G 5 HOH A 58 1158 320 HOH HOH . G 5 HOH A 59 1159 46 HOH HOH . G 5 HOH A 60 1160 159 HOH HOH . G 5 HOH A 61 1161 3 HOH HOH . G 5 HOH A 62 1162 249 HOH HOH . G 5 HOH A 63 1163 229 HOH HOH . G 5 HOH A 64 1164 51 HOH HOH . G 5 HOH A 65 1165 27 HOH HOH . G 5 HOH A 66 1166 284 HOH HOH . G 5 HOH A 67 1167 218 HOH HOH . G 5 HOH A 68 1168 36 HOH HOH . G 5 HOH A 69 1169 2 HOH HOH . G 5 HOH A 70 1170 150 HOH HOH . G 5 HOH A 71 1171 322 HOH HOH . G 5 HOH A 72 1172 98 HOH HOH . G 5 HOH A 73 1173 84 HOH HOH . G 5 HOH A 74 1174 83 HOH HOH . G 5 HOH A 75 1175 37 HOH HOH . G 5 HOH A 76 1176 192 HOH HOH . G 5 HOH A 77 1177 74 HOH HOH . G 5 HOH A 78 1178 221 HOH HOH . G 5 HOH A 79 1179 224 HOH HOH . G 5 HOH A 80 1180 161 HOH HOH . G 5 HOH A 81 1181 79 HOH HOH . G 5 HOH A 82 1182 243 HOH HOH . G 5 HOH A 83 1183 212 HOH HOH . G 5 HOH A 84 1184 317 HOH HOH . G 5 HOH A 85 1185 283 HOH HOH . G 5 HOH A 86 1186 24 HOH HOH . G 5 HOH A 87 1187 260 HOH HOH . G 5 HOH A 88 1188 194 HOH HOH . G 5 HOH A 89 1189 180 HOH HOH . H 5 HOH B 1 1101 262 HOH HOH . H 5 HOH B 2 1102 23 HOH HOH . H 5 HOH B 3 1103 278 HOH HOH . H 5 HOH B 4 1104 7 HOH HOH . H 5 HOH B 5 1105 26 HOH HOH . H 5 HOH B 6 1106 165 HOH HOH . H 5 HOH B 7 1107 173 HOH HOH . H 5 HOH B 8 1108 54 HOH HOH . H 5 HOH B 9 1109 15 HOH HOH . H 5 HOH B 10 1110 199 HOH HOH . H 5 HOH B 11 1111 135 HOH HOH . H 5 HOH B 12 1112 163 HOH HOH . H 5 HOH B 13 1113 213 HOH HOH . H 5 HOH B 14 1114 185 HOH HOH . H 5 HOH B 15 1115 125 HOH HOH . H 5 HOH B 16 1116 288 HOH HOH . H 5 HOH B 17 1117 279 HOH HOH . H 5 HOH B 18 1118 53 HOH HOH . H 5 HOH B 19 1119 206 HOH HOH . H 5 HOH B 20 1120 269 HOH HOH . H 5 HOH B 21 1121 40 HOH HOH . H 5 HOH B 22 1122 175 HOH HOH . H 5 HOH B 23 1123 203 HOH HOH . H 5 HOH B 24 1124 111 HOH HOH . H 5 HOH B 25 1125 244 HOH HOH . H 5 HOH B 26 1126 28 HOH HOH . H 5 HOH B 27 1127 197 HOH HOH . H 5 HOH B 28 1128 240 HOH HOH . H 5 HOH B 29 1129 189 HOH HOH . H 5 HOH B 30 1130 191 HOH HOH . H 5 HOH B 31 1131 61 HOH HOH . H 5 HOH B 32 1132 210 HOH HOH . H 5 HOH B 33 1133 20 HOH HOH . H 5 HOH B 34 1134 156 HOH HOH . H 5 HOH B 35 1135 102 HOH HOH . H 5 HOH B 36 1136 207 HOH HOH . H 5 HOH B 37 1137 234 HOH HOH . H 5 HOH B 38 1138 158 HOH HOH . H 5 HOH B 39 1139 198 HOH HOH . H 5 HOH B 40 1140 52 HOH HOH . H 5 HOH B 41 1141 167 HOH HOH . H 5 HOH B 42 1142 193 HOH HOH . H 5 HOH B 43 1143 48 HOH HOH . H 5 HOH B 44 1144 8 HOH HOH . H 5 HOH B 45 1145 69 HOH HOH . H 5 HOH B 46 1146 6 HOH HOH . H 5 HOH B 47 1147 182 HOH HOH . H 5 HOH B 48 1148 223 HOH HOH . H 5 HOH B 49 1149 35 HOH HOH . H 5 HOH B 50 1150 112 HOH HOH . H 5 HOH B 51 1151 14 HOH HOH . H 5 HOH B 52 1152 110 HOH HOH . H 5 HOH B 53 1153 117 HOH HOH . H 5 HOH B 54 1154 93 HOH HOH . H 5 HOH B 55 1155 134 HOH HOH . H 5 HOH B 56 1156 220 HOH HOH . H 5 HOH B 57 1157 263 HOH HOH . H 5 HOH B 58 1158 289 HOH HOH . H 5 HOH B 59 1159 12 HOH HOH . H 5 HOH B 60 1160 108 HOH HOH . H 5 HOH B 61 1161 25 HOH HOH . H 5 HOH B 62 1162 280 HOH HOH . H 5 HOH B 63 1163 296 HOH HOH . H 5 HOH B 64 1164 211 HOH HOH . H 5 HOH B 65 1165 5 HOH HOH . H 5 HOH B 66 1166 247 HOH HOH . H 5 HOH B 67 1167 100 HOH HOH . H 5 HOH B 68 1168 141 HOH HOH . H 5 HOH B 69 1169 291 HOH HOH . H 5 HOH B 70 1170 295 HOH HOH . H 5 HOH B 71 1171 31 HOH HOH . H 5 HOH B 72 1172 181 HOH HOH . H 5 HOH B 73 1173 219 HOH HOH . H 5 HOH B 74 1174 57 HOH HOH . H 5 HOH B 75 1175 179 HOH HOH . H 5 HOH B 76 1176 144 HOH HOH . H 5 HOH B 77 1177 82 HOH HOH . H 5 HOH B 78 1178 59 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 PLP . . . D 3 50.524 27.316 53.538 1 35.79 ? N1 PLP 1001 A 1 HETATM 2 C C2 PLP . . . D 3 49.375 26.677 53.295 1 35.88 ? C2 PLP 1001 A 1 HETATM 3 C C2A PLP . . . D 3 48.583 27.158 52.118 1 36.04 ? C2A PLP 1001 A 1 HETATM 4 C C3 PLP . . . D 3 48.879 25.666 54.134 1 36.17 ? C3 PLP 1001 A 1 HETATM 5 O O3 PLP . . . D 3 47.566 25.285 54.006 1 36.03 ? O3 PLP 1001 A 1 HETATM 6 C C4 PLP . . . D 3 49.597 25.366 55.309 1 36.84 ? C4 PLP 1001 A 1 HETATM 7 C C4A PLP . . . D 3 49.09 24.356 56.263 1 38.14 ? C4A PLP 1001 A 1 HETATM 8 C C5 PLP . . . D 3 50.783 26.083 55.577 1 35.86 ? C5 PLP 1001 A 1 HETATM 9 C C6 PLP . . . D 3 51.194 27.011 54.653 1 35.82 ? C6 PLP 1001 A 1 HETATM 10 C C5A PLP . . . D 3 51.559 25.932 56.856 1 34.91 ? C5A PLP 1001 A 1 HETATM 11 O O4P PLP . . . D 3 52.259 24.678 56.857 1 34.01 ? O4P PLP 1001 A 1 HETATM 12 P P PLP . . . D 3 52.32 23.79 58.191 1 32.96 ? P PLP 1001 A 1 HETATM 13 O O1P PLP . . . D 3 52.956 22.448 57.917 1 32.58 ? O1P PLP 1001 A 1 HETATM 14 O O2P PLP . . . D 3 53.077 24.68 59.183 1 32.71 ? O2P PLP 1001 A 1 HETATM 15 O O3P PLP . . . D 3 50.884 23.631 58.63 1 32.95 ? O3P PLP 1001 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #