data_1X28 # _model_server_result.job_id gGtT7e720OSEVpsBUe5i1w _model_server_result.datetime_utc '2024-11-24 23:41:59' _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":"D","auth_seq_id":1413}' # _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 . . . D 2 40.731 104.333 -11.118 1 28.52 ? N1 PGU 1413 B 1 HETATM 2 C C2 PGU . . . D 2 40.242 105.493 -11.721 1 29.61 ? C2 PGU 1413 B 1 HETATM 3 C C2A PGU . . . D 2 41.283 106.59 -11.596 1 27.55 ? C2A PGU 1413 B 1 HETATM 4 C C3 PGU . . . D 2 38.901 105.443 -12.326 1 29.57 ? C3 PGU 1413 B 1 HETATM 5 O O3 PGU . . . D 2 38.556 106.644 -12.876 1 31.28 ? O3 PGU 1413 B 1 HETATM 6 C C4 PGU . . . D 2 38.086 104.271 -12.322 1 28.59 ? C4 PGU 1413 B 1 HETATM 7 C C4A PGU . . . D 2 36.683 104.244 -12.964 1 30.36 ? C4A PGU 1413 B 1 HETATM 8 C C5 PGU . . . D 2 38.741 103.15 -11.655 1 26.21 ? C5 PGU 1413 B 1 HETATM 9 C C6 PGU . . . D 2 40.011 103.167 -11.072 1 27.31 ? C6 PGU 1413 B 1 HETATM 10 C C5A PGU . . . D 2 38.095 101.772 -11.508 1 24.18 ? C5A PGU 1413 B 1 HETATM 11 O O4P PGU . . . D 2 37.799 101.094 -12.67 1 24.32 ? O4P PGU 1413 B 1 HETATM 12 P P PGU . . . D 2 36.969 99.721 -12.76 1 23.24 ? P PGU 1413 B 1 HETATM 13 O O1P PGU . . . D 2 37.618 98.762 -13.614 1 22.28 ? O1P PGU 1413 B 1 HETATM 14 O O2P PGU . . . D 2 35.569 100.183 -13.094 1 21.38 ? O2P PGU 1413 B 1 HETATM 15 O O3P PGU . . . D 2 37.03 99.116 -11.368 1 24.73 ? O3P PGU 1413 B 1 HETATM 16 N N PGU . . . D 2 36.06 105.601 -12.592 1 34.96 ? N PGU 1413 B 1 HETATM 17 C CA PGU . . . D 2 34.87 105.976 -13.483 1 32.49 ? CA PGU 1413 B 1 HETATM 18 C CB PGU . . . D 2 33.764 104.897 -13.426 1 35.59 ? CB PGU 1413 B 1 HETATM 19 C CG PGU . . . D 2 32.839 104.865 -12.185 1 40.24 ? CG PGU 1413 B 1 HETATM 20 C CD PGU . . . D 2 33.589 104.682 -10.863 1 41.65 ? CD PGU 1413 B 1 HETATM 21 O OE1 PGU . . . D 2 33.554 105.624 -10.117 1 42.84 ? OE1 PGU 1413 B 1 HETATM 22 O OE2 PGU . . . D 2 34.144 103.578 -10.729 1 46.56 ? OE2 PGU 1413 B 1 HETATM 23 C C PGU . . . D 2 34.317 107.367 -13.058 1 29.25 ? C PGU 1413 B 1 HETATM 24 O O PGU . . . D 2 35.153 107.982 -12.186 1 29.4 ? O PGU 1413 B 1 HETATM 25 O OXT PGU . . . D 2 33.188 107.879 -13.464 1 28.62 ? OXT PGU 1413 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #