data_1X2A
#
_model_server_result.job_id            Fq4BjujBnhdTfIm9levl6w 
_model_server_result.datetime_utc      '2024-11-25 17:37:36' 
_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          1x2a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1413}' 
#
_entry.id    1X2A 
#
_exptl.entry_id    1X2A 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              378.272 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID' 
_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         120 
_cell.entry_id            1X2A 
_cell.length_a            142.71 
_cell.length_b            142.71 
_cell.length_c            81.39 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1X2A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_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 
_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
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C13 H19 N2 O9 P' 
_chem_comp.formula_weight    378.272 
_chem_comp.id                PDG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE" 
#
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 PDG doub 237 n y 
N1 C6 PDG sing 238 n y 
C2 C2A PDG sing 239 n n 
C2 C3 PDG sing 240 n y 
C2A H2A1 PDG sing 241 n n 
C2A H2A2 PDG sing 242 n n 
C2A H2A3 PDG sing 243 n n 
C3 O3 PDG sing 244 n n 
C3 C4 PDG doub 245 n y 
O3 HO3 PDG sing 246 n n 
C4 C4A PDG sing 247 n n 
C4 C5 PDG sing 248 n y 
C4A NA PDG sing 249 n n 
C4A H4A1 PDG sing 250 n n 
C4A H4A2 PDG sing 251 n n 
C5 C6 PDG doub 252 n y 
C5 C5A PDG sing 253 n n 
C6 H6 PDG sing 254 n n 
C5A OP4 PDG sing 255 n n 
C5A H5A1 PDG sing 256 n n 
C5A H5A2 PDG sing 257 n n 
OP4 P PDG sing 258 n n 
P OP1 PDG doub 259 n n 
P OP2 PDG sing 260 n n 
P OP3 PDG sing 261 n n 
OP2 HP2 PDG sing 262 n n 
OP3 HP3 PDG sing 263 n n 
NA CAA PDG sing 264 n n 
NA HNA PDG sing 265 n n 
CAA CBA PDG sing 266 n n 
CAA CA PDG sing 267 n n 
CAA HAA PDG sing 268 n n 
CBA CGA PDG sing 269 n n 
CBA HBA1 PDG sing 270 n n 
CBA HBA2 PDG sing 271 n n 
CGA CDA PDG sing 272 n n 
CGA HGA1 PDG sing 273 n n 
CGA HGA2 PDG sing 274 n n 
CDA OE1 PDG sing 275 n n 
CDA OE2 PDG doub 276 n n 
OE1 HE1 PDG sing 277 n n 
CA OA PDG doub 278 n n 
CA OXT PDG sing 279 n n 
OXT HXT PDG sing 280 n n 
#
_atom_sites.entry_id                     1X2A 
_atom_sites.fract_transf_matrix[1][1]    0.007007 
_atom_sites.fract_transf_matrix[1][2]    0.004046 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008091 
_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]    0.012287 
_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 PDG A 1 413 413 PDG PDE . 
D 2 PDG B 1 1413 1413 PDG PDE . 
E 3 HOH A 1 414 2 HOH HOH . 
E 3 HOH A 2 415 3 HOH HOH . 
E 3 HOH A 3 416 5 HOH HOH . 
E 3 HOH A 4 417 7 HOH HOH . 
E 3 HOH A 5 418 8 HOH HOH . 
E 3 HOH A 6 419 9 HOH HOH . 
E 3 HOH A 7 420 10 HOH HOH . 
E 3 HOH A 8 421 11 HOH HOH . 
E 3 HOH A 9 422 12 HOH HOH . 
E 3 HOH A 10 423 14 HOH HOH . 
E 3 HOH A 11 424 16 HOH HOH . 
E 3 HOH A 12 425 17 HOH HOH . 
E 3 HOH A 13 426 18 HOH HOH . 
E 3 HOH A 14 427 21 HOH HOH . 
E 3 HOH A 15 428 22 HOH HOH . 
E 3 HOH A 16 429 23 HOH HOH . 
E 3 HOH A 17 430 25 HOH HOH . 
E 3 HOH A 18 431 27 HOH HOH . 
E 3 HOH A 19 432 30 HOH HOH . 
E 3 HOH A 20 433 31 HOH HOH . 
E 3 HOH A 21 434 32 HOH HOH . 
E 3 HOH A 22 435 36 HOH HOH . 
E 3 HOH A 23 436 39 HOH HOH . 
E 3 HOH A 24 437 41 HOH HOH . 
E 3 HOH A 25 438 42 HOH HOH . 
E 3 HOH A 26 439 45 HOH HOH . 
E 3 HOH A 27 440 47 HOH HOH . 
E 3 HOH A 28 441 48 HOH HOH . 
E 3 HOH A 29 442 49 HOH HOH . 
E 3 HOH A 30 443 51 HOH HOH . 
E 3 HOH A 31 444 52 HOH HOH . 
E 3 HOH A 32 445 54 HOH HOH . 
E 3 HOH A 33 446 55 HOH HOH . 
E 3 HOH A 34 447 56 HOH HOH . 
E 3 HOH A 35 448 57 HOH HOH . 
E 3 HOH A 36 449 60 HOH HOH . 
E 3 HOH A 37 450 63 HOH HOH . 
E 3 HOH A 38 451 64 HOH HOH . 
E 3 HOH A 39 452 65 HOH HOH . 
E 3 HOH A 40 453 66 HOH HOH . 
E 3 HOH A 41 454 69 HOH HOH . 
E 3 HOH A 42 455 70 HOH HOH . 
E 3 HOH A 43 456 71 HOH HOH . 
E 3 HOH A 44 457 73 HOH HOH . 
E 3 HOH A 45 458 74 HOH HOH . 
E 3 HOH A 46 459 75 HOH HOH . 
E 3 HOH A 47 460 77 HOH HOH . 
E 3 HOH A 48 461 79 HOH HOH . 
E 3 HOH A 49 462 80 HOH HOH . 
E 3 HOH A 50 463 81 HOH HOH . 
E 3 HOH A 51 464 83 HOH HOH . 
E 3 HOH A 52 465 85 HOH HOH . 
E 3 HOH A 53 466 86 HOH HOH . 
E 3 HOH A 54 467 88 HOH HOH . 
E 3 HOH A 55 468 89 HOH HOH . 
E 3 HOH A 56 469 90 HOH HOH . 
E 3 HOH A 57 470 93 HOH HOH . 
E 3 HOH A 58 471 94 HOH HOH . 
E 3 HOH A 59 472 95 HOH HOH . 
E 3 HOH A 60 473 97 HOH HOH . 
E 3 HOH A 61 474 101 HOH HOH . 
E 3 HOH A 62 475 102 HOH HOH . 
E 3 HOH A 63 476 109 HOH HOH . 
E 3 HOH A 64 477 110 HOH HOH . 
E 3 HOH A 65 478 111 HOH HOH . 
E 3 HOH A 66 479 113 HOH HOH . 
E 3 HOH A 67 480 119 HOH HOH . 
E 3 HOH A 68 481 120 HOH HOH . 
E 3 HOH A 69 482 122 HOH HOH . 
E 3 HOH A 70 483 123 HOH HOH . 
E 3 HOH A 71 484 124 HOH HOH . 
E 3 HOH A 72 485 125 HOH HOH . 
E 3 HOH A 73 486 128 HOH HOH . 
E 3 HOH A 74 487 129 HOH HOH . 
E 3 HOH A 75 488 134 HOH HOH . 
E 3 HOH A 76 489 136 HOH HOH . 
E 3 HOH A 77 490 137 HOH HOH . 
E 3 HOH A 78 491 138 HOH HOH . 
E 3 HOH A 79 492 142 HOH HOH . 
E 3 HOH A 80 493 144 HOH HOH . 
E 3 HOH A 81 494 145 HOH HOH . 
E 3 HOH A 82 495 146 HOH HOH . 
E 3 HOH A 83 496 148 HOH HOH . 
E 3 HOH A 84 497 149 HOH HOH . 
E 3 HOH A 85 498 151 HOH HOH . 
E 3 HOH A 86 499 154 HOH HOH . 
E 3 HOH A 87 500 155 HOH HOH . 
E 3 HOH A 88 501 156 HOH HOH . 
E 3 HOH A 89 502 157 HOH HOH . 
E 3 HOH A 90 503 159 HOH HOH . 
E 3 HOH A 91 504 160 HOH HOH . 
E 3 HOH A 92 505 161 HOH HOH . 
E 3 HOH A 93 506 162 HOH HOH . 
E 3 HOH A 94 507 163 HOH HOH . 
E 3 HOH A 95 508 164 HOH HOH . 
E 3 HOH A 96 509 167 HOH HOH . 
E 3 HOH A 97 510 170 HOH HOH . 
E 3 HOH A 98 511 171 HOH HOH . 
E 3 HOH A 99 512 172 HOH HOH . 
E 3 HOH A 100 513 174 HOH HOH . 
E 3 HOH A 101 514 177 HOH HOH . 
E 3 HOH A 102 515 178 HOH HOH . 
E 3 HOH A 103 516 180 HOH HOH . 
E 3 HOH A 104 517 181 HOH HOH . 
E 3 HOH A 105 518 182 HOH HOH . 
E 3 HOH A 106 519 185 HOH HOH . 
E 3 HOH A 107 520 186 HOH HOH . 
E 3 HOH A 108 521 188 HOH HOH . 
E 3 HOH A 109 522 189 HOH HOH . 
E 3 HOH A 110 523 191 HOH HOH . 
E 3 HOH A 111 524 194 HOH HOH . 
E 3 HOH A 112 525 195 HOH HOH . 
E 3 HOH A 113 526 200 HOH HOH . 
E 3 HOH A 114 527 201 HOH HOH . 
E 3 HOH A 115 528 203 HOH HOH . 
F 3 HOH B 1 1414 1 HOH HOH . 
F 3 HOH B 2 1415 4 HOH HOH . 
F 3 HOH B 3 1416 6 HOH HOH . 
F 3 HOH B 4 1417 13 HOH HOH . 
F 3 HOH B 5 1418 15 HOH HOH . 
F 3 HOH B 6 1419 19 HOH HOH . 
F 3 HOH B 7 1420 20 HOH HOH . 
F 3 HOH B 8 1421 24 HOH HOH . 
F 3 HOH B 9 1422 26 HOH HOH . 
F 3 HOH B 10 1423 28 HOH HOH . 
F 3 HOH B 11 1424 29 HOH HOH . 
F 3 HOH B 12 1425 33 HOH HOH . 
F 3 HOH B 13 1426 34 HOH HOH . 
F 3 HOH B 14 1427 35 HOH HOH . 
F 3 HOH B 15 1428 37 HOH HOH . 
F 3 HOH B 16 1429 38 HOH HOH . 
F 3 HOH B 17 1430 40 HOH HOH . 
F 3 HOH B 18 1431 43 HOH HOH . 
F 3 HOH B 19 1432 44 HOH HOH . 
F 3 HOH B 20 1433 46 HOH HOH . 
F 3 HOH B 21 1434 50 HOH HOH . 
F 3 HOH B 22 1435 53 HOH HOH . 
F 3 HOH B 23 1436 58 HOH HOH . 
F 3 HOH B 24 1437 59 HOH HOH . 
F 3 HOH B 25 1438 61 HOH HOH . 
F 3 HOH B 26 1439 62 HOH HOH . 
F 3 HOH B 27 1440 67 HOH HOH . 
F 3 HOH B 28 1441 68 HOH HOH . 
F 3 HOH B 29 1442 72 HOH HOH . 
F 3 HOH B 30 1443 76 HOH HOH . 
F 3 HOH B 31 1444 78 HOH HOH . 
F 3 HOH B 32 1445 82 HOH HOH . 
F 3 HOH B 33 1446 84 HOH HOH . 
F 3 HOH B 34 1447 87 HOH HOH . 
F 3 HOH B 35 1448 91 HOH HOH . 
F 3 HOH B 36 1449 92 HOH HOH . 
F 3 HOH B 37 1450 96 HOH HOH . 
F 3 HOH B 38 1451 98 HOH HOH . 
F 3 HOH B 39 1452 99 HOH HOH . 
F 3 HOH B 40 1453 100 HOH HOH . 
F 3 HOH B 41 1454 103 HOH HOH . 
F 3 HOH B 42 1455 104 HOH HOH . 
F 3 HOH B 43 1456 105 HOH HOH . 
F 3 HOH B 44 1457 106 HOH HOH . 
F 3 HOH B 45 1458 107 HOH HOH . 
F 3 HOH B 46 1459 108 HOH HOH . 
F 3 HOH B 47 1460 112 HOH HOH . 
F 3 HOH B 48 1461 114 HOH HOH . 
F 3 HOH B 49 1462 115 HOH HOH . 
F 3 HOH B 50 1463 116 HOH HOH . 
F 3 HOH B 51 1464 117 HOH HOH . 
F 3 HOH B 52 1465 118 HOH HOH . 
F 3 HOH B 53 1466 121 HOH HOH . 
F 3 HOH B 54 1467 126 HOH HOH . 
F 3 HOH B 55 1468 127 HOH HOH . 
F 3 HOH B 56 1469 130 HOH HOH . 
F 3 HOH B 57 1470 131 HOH HOH . 
F 3 HOH B 58 1471 132 HOH HOH . 
F 3 HOH B 59 1472 133 HOH HOH . 
F 3 HOH B 60 1473 135 HOH HOH . 
F 3 HOH B 61 1474 139 HOH HOH . 
F 3 HOH B 62 1475 140 HOH HOH . 
F 3 HOH B 63 1476 141 HOH HOH . 
F 3 HOH B 64 1477 143 HOH HOH . 
F 3 HOH B 65 1478 147 HOH HOH . 
F 3 HOH B 66 1479 150 HOH HOH . 
F 3 HOH B 67 1480 152 HOH HOH . 
F 3 HOH B 68 1481 153 HOH HOH . 
F 3 HOH B 69 1482 158 HOH HOH . 
F 3 HOH B 70 1483 165 HOH HOH . 
F 3 HOH B 71 1484 166 HOH HOH . 
F 3 HOH B 72 1485 168 HOH HOH . 
F 3 HOH B 73 1486 169 HOH HOH . 
F 3 HOH B 74 1487 173 HOH HOH . 
F 3 HOH B 75 1488 175 HOH HOH . 
F 3 HOH B 76 1489 176 HOH HOH . 
F 3 HOH B 77 1490 179 HOH HOH . 
F 3 HOH B 78 1491 183 HOH HOH . 
F 3 HOH B 79 1492 184 HOH HOH . 
F 3 HOH B 80 1493 187 HOH HOH . 
F 3 HOH B 81 1494 190 HOH HOH . 
F 3 HOH B 82 1495 192 HOH HOH . 
F 3 HOH B 83 1496 193 HOH HOH . 
F 3 HOH B 84 1497 196 HOH HOH . 
F 3 HOH B 85 1498 197 HOH HOH . 
F 3 HOH B 86 1499 198 HOH HOH . 
F 3 HOH B 87 1500 199 HOH HOH . 
F 3 HOH B 88 1501 202 HOH HOH . 
F 3 HOH B 89 1502 204 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 PDG . . . D 2 40.416 103.523 -11.097 1 28.18 ? N1 PDG 1413 B 1 
HETATM 2 C C2 PDG . . . D 2 40.019 104.639 -11.827 1 29.97 ? C2 PDG 1413 B 1 
HETATM 3 C C2A PDG . . . D 2 41.074 105.728 -11.68 1 27.9 ? C2A PDG 1413 B 1 
HETATM 4 C C3 PDG . . . D 2 38.744 104.567 -12.556 1 27.84 ? C3 PDG 1413 B 1 
HETATM 5 O O3 PDG . . . D 2 38.501 105.724 -13.213 1 28.5 ? O3 PDG 1413 B 1 
HETATM 6 C C4 PDG . . . D 2 37.898 103.406 -12.548 1 28.51 ? C4 PDG 1413 B 1 
HETATM 7 C C4A PDG . . . D 2 36.555 103.313 -13.317 1 25.47 ? C4A PDG 1413 B 1 
HETATM 8 C C5 PDG . . . D 2 38.461 102.338 -11.739 1 26.85 ? C5 PDG 1413 B 1 
HETATM 9 C C6 PDG . . . D 2 39.668 102.378 -11.036 1 27.38 ? C6 PDG 1413 B 1 
HETATM 10 C C5A PDG . . . D 2 37.771 100.99 -11.557 1 25.68 ? C5A PDG 1413 B 1 
HETATM 11 O OP4 PDG . . . D 2 37.28 100.364 -12.678 1 23.31 ? OP4 PDG 1413 B 1 
HETATM 12 P P PDG . . . D 2 36.683 98.874 -12.691 1 23.33 ? P PDG 1413 B 1 
HETATM 13 O OP1 PDG . . . D 2 37.45 97.992 -13.527 1 20.33 ? OP1 PDG 1413 B 1 
HETATM 14 O OP2 PDG . . . D 2 35.213 99.104 -12.989 1 22.65 ? OP2 PDG 1413 B 1 
HETATM 15 O OP3 PDG . . . D 2 36.879 98.35 -11.278 1 20.1 ? OP3 PDG 1413 B 1 
HETATM 16 N NA PDG . . . D 2 36.052 104.742 -13.471 1 29.17 ? NA PDG 1413 B 1 
HETATM 17 C CAA PDG . . . D 2 34.774 104.984 -12.697 1 27.45 ? CAA PDG 1413 B 1 
HETATM 18 C CBA PDG . . . D 2 33.631 104.021 -13.087 1 25.49 ? CBA PDG 1413 B 1 
HETATM 19 C CGA PDG . . . D 2 32.447 103.935 -12.1 1 26.05 ? CGA PDG 1413 B 1 
HETATM 20 C CDA PDG . . . D 2 32.901 103.755 -10.641 1 26.29 ? CDA PDG 1413 B 1 
HETATM 21 O OE1 PDG . . . D 2 32.918 104.757 -9.967 1 23.99 ? OE1 PDG 1413 B 1 
HETATM 22 O OE2 PDG . . . D 2 33.193 102.587 -10.337 1 27.33 ? OE2 PDG 1413 B 1 
HETATM 23 C CA PDG . . . D 2 34.373 106.454 -12.898 1 27.81 ? CA PDG 1413 B 1 
HETATM 24 O OA PDG . . . D 2 35.366 107.256 -12.436 1 28.99 ? OA PDG 1413 B 1 
HETATM 25 O OXT PDG . . . D 2 33.249 106.881 -13.436 1 26.66 ? OXT PDG 1413 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          26 
_model_server_stats.element_count           25 
#