data_7QGT
#
_model_server_result.job_id            jUe_W0TkOhsBa3xXaTITNg 
_model_server_result.datetime_utc      '2024-11-26 03:31:53' 
_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              23 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#