data_1X28
#
_model_server_result.job_id            QynHnDSSB_S7cvWQRhZIhA 
_model_server_result.datetime_utc      '2024-10-25 20:29:54' 
_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          1x28 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":413}' 
#
_entry.id    1X28 
#
_exptl.entry_id    1X28 
_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)-L-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            1X28 
_cell.length_a            143.83 
_cell.length_b            143.83 
_cell.length_c            81.57 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1X28 
_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                PGU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid' 
_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
O1P P PGU doub 237 n n 
CA CB PGU sing 238 n n 
CA C PGU sing 239 n n 
CA N PGU sing 240 n n 
OXT C PGU doub 241 n n 
CB CG PGU sing 242 n n 
O2P P PGU sing 243 n n 
C O PGU sing 244 n n 
C4A N PGU sing 245 n n 
C4A C4 PGU sing 246 n n 
O3 C3 PGU sing 247 n n 
P O4P PGU sing 248 n n 
P O3P PGU sing 249 n n 
O4P C5A PGU sing 250 n n 
C3 C4 PGU doub 251 n y 
C3 C2 PGU sing 252 n y 
C4 C5 PGU sing 253 n y 
CG CD PGU sing 254 n n 
C2 C2A PGU sing 255 n n 
C2 N1 PGU doub 256 n y 
C5 C5A PGU sing 257 n n 
C5 C6 PGU doub 258 n y 
N1 C6 PGU sing 259 n y 
CD OE2 PGU doub 260 n n 
CD OE1 PGU sing 261 n n 
C2A H2A1 PGU sing 262 n n 
C2A H2A2 PGU sing 263 n n 
C2A H2A3 PGU sing 264 n n 
O3 HO3 PGU sing 265 n n 
C4A H4A1 PGU sing 266 n n 
C4A H4A2 PGU sing 267 n n 
C6 H6 PGU sing 268 n n 
C5A H5A1 PGU sing 269 n n 
C5A H5A2 PGU sing 270 n n 
O2P HO2P PGU sing 271 n n 
O3P HO3P PGU sing 272 n n 
N HN PGU sing 273 n n 
CA HA PGU sing 274 n n 
CB HB1 PGU sing 275 n n 
CB HB2 PGU sing 276 n n 
CG HG1 PGU sing 277 n n 
CG HG2 PGU sing 278 n n 
OE1 HOE1 PGU sing 279 n n 
O HO PGU sing 280 n n 
#
_atom_sites.entry_id                     1X28 
_atom_sites.fract_transf_matrix[1][1]    0.006953 
_atom_sites.fract_transf_matrix[1][2]    0.004014 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008028 
_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]    0.012259 
_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 PGU A 1 413 413 PGU PPE . 
D 2 PGU B 1 1413 1413 PGU PPE . 
E 3 HOH A 1 414 1 HOH HOH . 
E 3 HOH A 2 415 2 HOH HOH . 
E 3 HOH A 3 416 3 HOH HOH . 
E 3 HOH A 4 417 4 HOH HOH . 
E 3 HOH A 5 418 5 HOH HOH . 
E 3 HOH A 6 419 8 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 13 HOH HOH . 
E 3 HOH A 11 424 14 HOH HOH . 
E 3 HOH A 12 425 15 HOH HOH . 
E 3 HOH A 13 426 18 HOH HOH . 
E 3 HOH A 14 427 20 HOH HOH . 
E 3 HOH A 15 428 23 HOH HOH . 
E 3 HOH A 16 429 25 HOH HOH . 
E 3 HOH A 17 430 27 HOH HOH . 
E 3 HOH A 18 431 28 HOH HOH . 
E 3 HOH A 19 432 31 HOH HOH . 
E 3 HOH A 20 433 33 HOH HOH . 
E 3 HOH A 21 434 35 HOH HOH . 
E 3 HOH A 22 435 36 HOH HOH . 
E 3 HOH A 23 436 37 HOH HOH . 
E 3 HOH A 24 437 38 HOH HOH . 
E 3 HOH A 25 438 40 HOH HOH . 
E 3 HOH A 26 439 41 HOH HOH . 
E 3 HOH A 27 440 42 HOH HOH . 
E 3 HOH A 28 441 45 HOH HOH . 
E 3 HOH A 29 442 46 HOH HOH . 
E 3 HOH A 30 443 48 HOH HOH . 
E 3 HOH A 31 444 49 HOH HOH . 
E 3 HOH A 32 445 53 HOH HOH . 
E 3 HOH A 33 446 54 HOH HOH . 
E 3 HOH A 34 447 57 HOH HOH . 
E 3 HOH A 35 448 60 HOH HOH . 
E 3 HOH A 36 449 63 HOH HOH . 
E 3 HOH A 37 450 64 HOH HOH . 
E 3 HOH A 38 451 65 HOH HOH . 
E 3 HOH A 39 452 67 HOH HOH . 
E 3 HOH A 40 453 68 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 76 HOH HOH . 
E 3 HOH A 48 461 78 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 82 HOH HOH . 
E 3 HOH A 52 465 86 HOH HOH . 
E 3 HOH A 53 466 87 HOH HOH . 
E 3 HOH A 54 467 91 HOH HOH . 
E 3 HOH A 55 468 92 HOH HOH . 
E 3 HOH A 56 469 94 HOH HOH . 
E 3 HOH A 57 470 96 HOH HOH . 
E 3 HOH A 58 471 97 HOH HOH . 
E 3 HOH A 59 472 98 HOH HOH . 
E 3 HOH A 60 473 99 HOH HOH . 
E 3 HOH A 61 474 100 HOH HOH . 
E 3 HOH A 62 475 101 HOH HOH . 
E 3 HOH A 63 476 102 HOH HOH . 
E 3 HOH A 64 477 104 HOH HOH . 
E 3 HOH A 65 478 105 HOH HOH . 
E 3 HOH A 66 479 108 HOH HOH . 
E 3 HOH A 67 480 110 HOH HOH . 
E 3 HOH A 68 481 111 HOH HOH . 
E 3 HOH A 69 482 112 HOH HOH . 
E 3 HOH A 70 483 113 HOH HOH . 
E 3 HOH A 71 484 115 HOH HOH . 
E 3 HOH A 72 485 116 HOH HOH . 
E 3 HOH A 73 486 117 HOH HOH . 
E 3 HOH A 74 487 122 HOH HOH . 
E 3 HOH A 75 488 123 HOH HOH . 
E 3 HOH A 76 489 124 HOH HOH . 
E 3 HOH A 77 490 128 HOH HOH . 
F 3 HOH B 1 1414 6 HOH HOH . 
F 3 HOH B 2 1415 7 HOH HOH . 
F 3 HOH B 3 1416 9 HOH HOH . 
F 3 HOH B 4 1417 16 HOH HOH . 
F 3 HOH B 5 1418 17 HOH HOH . 
F 3 HOH B 6 1419 19 HOH HOH . 
F 3 HOH B 7 1420 21 HOH HOH . 
F 3 HOH B 8 1421 22 HOH HOH . 
F 3 HOH B 9 1422 24 HOH HOH . 
F 3 HOH B 10 1423 26 HOH HOH . 
F 3 HOH B 11 1424 29 HOH HOH . 
F 3 HOH B 12 1425 30 HOH HOH . 
F 3 HOH B 13 1426 32 HOH HOH . 
F 3 HOH B 14 1427 34 HOH HOH . 
F 3 HOH B 15 1428 39 HOH HOH . 
F 3 HOH B 16 1429 43 HOH HOH . 
F 3 HOH B 17 1430 44 HOH HOH . 
F 3 HOH B 18 1431 47 HOH HOH . 
F 3 HOH B 19 1432 50 HOH HOH . 
F 3 HOH B 20 1433 51 HOH HOH . 
F 3 HOH B 21 1434 52 HOH HOH . 
F 3 HOH B 22 1435 55 HOH HOH . 
F 3 HOH B 23 1436 56 HOH HOH . 
F 3 HOH B 24 1437 58 HOH HOH . 
F 3 HOH B 25 1438 59 HOH HOH . 
F 3 HOH B 26 1439 61 HOH HOH . 
F 3 HOH B 27 1440 62 HOH HOH . 
F 3 HOH B 28 1441 66 HOH HOH . 
F 3 HOH B 29 1442 72 HOH HOH . 
F 3 HOH B 30 1443 77 HOH HOH . 
F 3 HOH B 31 1444 79 HOH HOH . 
F 3 HOH B 32 1445 83 HOH HOH . 
F 3 HOH B 33 1446 84 HOH HOH . 
F 3 HOH B 34 1447 85 HOH HOH . 
F 3 HOH B 35 1448 88 HOH HOH . 
F 3 HOH B 36 1449 89 HOH HOH . 
F 3 HOH B 37 1450 90 HOH HOH . 
F 3 HOH B 38 1451 93 HOH HOH . 
F 3 HOH B 39 1452 95 HOH HOH . 
F 3 HOH B 40 1453 103 HOH HOH . 
F 3 HOH B 41 1454 106 HOH HOH . 
F 3 HOH B 42 1455 107 HOH HOH . 
F 3 HOH B 43 1456 109 HOH HOH . 
F 3 HOH B 44 1457 114 HOH HOH . 
F 3 HOH B 45 1458 118 HOH HOH . 
F 3 HOH B 46 1459 119 HOH HOH . 
F 3 HOH B 47 1460 120 HOH HOH . 
F 3 HOH B 48 1461 121 HOH HOH . 
F 3 HOH B 49 1462 125 HOH HOH . 
F 3 HOH B 50 1463 126 HOH HOH . 
F 3 HOH B 51 1464 127 HOH HOH . 
F 3 HOH B 52 1465 129 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 PGU . . . C 2 32.048 77.327 0.94 1 16.53 ? N1 PGU 413 A 1 
HETATM 2 C C2 PGU . . . C 2 32.246 75.944 0.896 1 17.29 ? C2 PGU 413 A 1 
HETATM 3 C C2A PGU . . . C 2 31.706 75.322 2.164 1 14.77 ? C2A PGU 413 A 1 
HETATM 4 C C3 PGU . . . C 2 32.895 75.384 -0.29 1 20.53 ? C3 PGU 413 A 1 
HETATM 5 O O3 PGU . . . C 2 33.019 74.037 -0.196 1 25.17 ? O3 PGU 413 A 1 
HETATM 6 C C4 PGU . . . C 2 33.331 76.179 -1.392 1 21.3 ? C4 PGU 413 A 1 
HETATM 7 C C4A PGU . . . C 2 34.003 75.566 -2.625 1 23.42 ? C4A PGU 413 A 1 
HETATM 8 C C5 PGU . . . C 2 33.056 77.593 -1.192 1 18.2 ? C5 PGU 413 A 1 
HETATM 9 C C6 PGU . . . C 2 32.437 78.16 -0.071 1 16.21 ? C6 PGU 413 A 1 
HETATM 10 C C5A PGU . . . C 2 33.424 78.667 -2.229 1 17.78 ? C5A PGU 413 A 1 
HETATM 11 O O4P PGU . . . C 2 32.605 78.773 -3.336 1 15.63 ? O4P PGU 413 A 1 
HETATM 12 P P PGU . . . C 2 32.941 79.617 -4.644 1 17.02 ? P PGU 413 A 1 
HETATM 13 O O1P PGU . . . C 2 31.755 79.993 -5.365 1 15.82 ? O1P PGU 413 A 1 
HETATM 14 O O2P PGU . . . C 2 33.992 78.789 -5.354 1 13.41 ? O2P PGU 413 A 1 
HETATM 15 O O3P PGU . . . C 2 33.507 80.918 -4.097 1 17.1 ? O3P PGU 413 A 1 
HETATM 16 N N PGU . . . C 2 35.019 74.571 -2.053 1 30.58 ? N PGU 413 A 1 
HETATM 17 C CA PGU . . . C 2 35.496 73.577 -3.111 1 33.67 ? CA PGU 413 A 1 
HETATM 18 C CB PGU . . . C 2 36.094 74.28 -4.37 1 35.57 ? CB PGU 413 A 1 
HETATM 19 C CG PGU . . . C 2 37.566 74.741 -4.356 1 38.93 ? CG PGU 413 A 1 
HETATM 20 C CD PGU . . . C 2 37.872 75.731 -3.234 1 40.98 ? CD PGU 413 A 1 
HETATM 21 O OE1 PGU . . . C 2 38.436 75.265 -2.262 1 38.97 ? OE1 PGU 413 A 1 
HETATM 22 O OE2 PGU . . . C 2 37.5 76.893 -3.471 1 41.81 ? OE2 PGU 413 A 1 
HETATM 23 C C PGU . . . C 2 36.493 72.589 -2.451 1 31.63 ? C PGU 413 A 1 
HETATM 24 O O PGU . . . C 2 36.189 72.424 -1.139 1 34.49 ? O PGU 413 A 1 
HETATM 25 O OXT PGU . . . C 2 37.482 71.988 -3.059 1 31.77 ? OXT PGU 413 A 1 
#
_model_server_stats.io_time_ms              38 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#