data_2ZPU # _model_server_result.job_id vu3i-w_MLHA3M_jyB8LSUg _model_server_result.datetime_utc '2025-02-18 09:52:53' _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 2zpu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":350}' # _entry.id 2ZPU # _exptl.entry_id 2ZPU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 320.236 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE" _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 102.41 _cell.angle_gamma 90 _cell.entry_id 2ZPU _cell.length_a 59.74 _cell.length_b 72.99 _cell.length_c 65.07 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZPU _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 45.756081 0 63.549625 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 57 A LYS 57 1_555 C CB PDD . A PDD 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? metalc ? metalc1 A OE2 GLU 208 A GLU 208 1_555 B MG MG . A MG 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc2 A O GLY 212 A GLY 212 1_555 B MG MG . A MG 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc3 A OD1 ASP 214 A ASP 214 1_555 B MG MG . A MG 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc4 B MG MG . A MG 360 1_555 D O HOH . A HOH 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc5 B MG MG . A MG 360 1_555 D O HOH . A HOH 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc6 B MG MG . A MG 360 1_555 D O HOH . A HOH 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? # _chem_comp.formula 'C11 H17 N2 O7 P' _chem_comp.formula_weight 320.236 _chem_comp.id PDD _chem_comp.mon_nstd_flag . _chem_comp.name "N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE" _chem_comp.type 'd-peptide linking' _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 N C4A PDD sing 237 n n N CA PDD sing 238 n n N H PDD sing 239 n n N1 C2 PDD doub 240 n y N1 C6 PDD sing 241 n y C2 C2A PDD sing 242 n n C2 C3 PDD sing 243 n y C2A H2A1 PDD sing 244 n n C2A H2A2 PDD sing 245 n n C2A H2A3 PDD sing 246 n n C3 O3A PDD sing 247 n n C3 C4 PDD doub 248 n y O3A HO3 PDD sing 249 n n C4 C4A PDD sing 250 n n C4 C5 PDD sing 251 n y C4A H4A1 PDD sing 252 n n C4A H4A2 PDD sing 253 n n C5 C5A PDD sing 254 n n C5 C6 PDD doub 255 n y C5A OP4 PDD sing 256 n n C5A H5A1 PDD sing 257 n n C5A H5A2 PDD sing 258 n n OP4 P PDD sing 259 n n P OP1 PDD doub 260 n n P OP2 PDD sing 261 n n P OP3 PDD sing 262 n n OP2 HOP2 PDD sing 263 n n OP3 HOP3 PDD sing 264 n n C6 H6 PDD sing 265 n n CA CB PDD sing 266 n n CA C PDD sing 267 n n CA HA PDD sing 268 n n CB HB1 PDD sing 269 n n CB HB2 PDD sing 270 n n CB HB3 PDD sing 271 n n C O PDD doub 272 n n C OXT PDD sing 273 n n OXT HXT PDD sing 274 n n # _atom_sites.entry_id 2ZPU _atom_sites.fract_transf_matrix[1][1] 0.016739 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003683 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013701 _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] 0.015736 _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 B 2 MG A 1 360 360 MG MG . C 3 PDD A 1 350 350 PDD PLS . D 4 HOH A 1 361 1 HOH HOH . D 4 HOH A 2 362 2 HOH HOH . D 4 HOH A 3 363 3 HOH HOH . D 4 HOH A 4 364 4 HOH HOH . D 4 HOH A 5 365 5 HOH HOH . D 4 HOH A 6 366 6 HOH HOH . D 4 HOH A 7 367 7 HOH HOH . D 4 HOH A 8 368 8 HOH HOH . D 4 HOH A 9 369 9 HOH HOH . D 4 HOH A 10 370 10 HOH HOH . D 4 HOH A 11 371 11 HOH HOH . D 4 HOH A 12 372 12 HOH HOH . D 4 HOH A 13 373 13 HOH HOH . D 4 HOH A 14 374 14 HOH HOH . D 4 HOH A 15 375 15 HOH HOH . D 4 HOH A 16 376 16 HOH HOH . D 4 HOH A 17 377 17 HOH HOH . D 4 HOH A 18 378 18 HOH HOH . D 4 HOH A 19 379 19 HOH HOH . D 4 HOH A 20 380 20 HOH HOH . D 4 HOH A 21 381 21 HOH HOH . D 4 HOH A 22 382 22 HOH HOH . D 4 HOH A 23 383 23 HOH HOH . D 4 HOH A 24 384 24 HOH HOH . D 4 HOH A 25 385 25 HOH HOH . D 4 HOH A 26 386 26 HOH HOH . D 4 HOH A 27 387 27 HOH HOH . D 4 HOH A 28 388 28 HOH HOH . D 4 HOH A 29 389 29 HOH HOH . D 4 HOH A 30 390 30 HOH HOH . D 4 HOH A 31 391 31 HOH HOH . D 4 HOH A 32 392 32 HOH HOH . D 4 HOH A 33 393 33 HOH HOH . D 4 HOH A 34 394 34 HOH HOH . D 4 HOH A 35 395 35 HOH HOH . D 4 HOH A 36 396 36 HOH HOH . D 4 HOH A 37 397 37 HOH HOH . D 4 HOH A 38 398 38 HOH HOH . D 4 HOH A 39 399 39 HOH HOH . D 4 HOH A 40 400 40 HOH HOH . D 4 HOH A 41 401 41 HOH HOH . D 4 HOH A 42 402 42 HOH HOH . D 4 HOH A 43 403 43 HOH HOH . D 4 HOH A 44 404 44 HOH HOH . D 4 HOH A 45 405 45 HOH HOH . D 4 HOH A 46 406 46 HOH HOH . D 4 HOH A 47 407 47 HOH HOH . D 4 HOH A 48 408 48 HOH HOH . D 4 HOH A 49 409 49 HOH HOH . D 4 HOH A 50 410 50 HOH HOH . D 4 HOH A 51 411 51 HOH HOH . D 4 HOH A 52 412 52 HOH HOH . D 4 HOH A 53 413 53 HOH HOH . D 4 HOH A 54 414 54 HOH HOH . D 4 HOH A 55 415 55 HOH HOH . D 4 HOH A 56 416 56 HOH HOH . D 4 HOH A 57 417 57 HOH HOH . D 4 HOH A 58 418 58 HOH HOH . D 4 HOH A 59 419 59 HOH HOH . D 4 HOH A 60 420 60 HOH HOH . D 4 HOH A 61 421 61 HOH HOH . D 4 HOH A 62 422 62 HOH HOH . D 4 HOH A 63 423 63 HOH HOH . D 4 HOH A 64 424 64 HOH HOH . D 4 HOH A 65 425 65 HOH HOH . D 4 HOH A 66 426 66 HOH HOH . D 4 HOH A 67 427 67 HOH HOH . D 4 HOH A 68 428 68 HOH HOH . D 4 HOH A 69 429 69 HOH HOH . D 4 HOH A 70 430 70 HOH HOH . D 4 HOH A 71 431 71 HOH HOH . D 4 HOH A 72 432 72 HOH HOH . D 4 HOH A 73 433 73 HOH HOH . D 4 HOH A 74 434 74 HOH HOH . D 4 HOH A 75 435 75 HOH HOH . D 4 HOH A 76 436 76 HOH HOH . D 4 HOH A 77 437 77 HOH HOH . D 4 HOH A 78 438 78 HOH HOH . D 4 HOH A 79 439 79 HOH HOH . D 4 HOH A 80 440 80 HOH HOH . D 4 HOH A 81 441 81 HOH HOH . D 4 HOH A 82 442 82 HOH HOH . D 4 HOH A 83 443 83 HOH HOH . D 4 HOH A 84 444 84 HOH HOH . D 4 HOH A 85 445 85 HOH HOH . D 4 HOH A 86 446 86 HOH HOH . D 4 HOH A 87 447 87 HOH HOH . D 4 HOH A 88 448 88 HOH HOH . D 4 HOH A 89 449 89 HOH HOH . D 4 HOH A 90 450 90 HOH HOH . D 4 HOH A 91 451 91 HOH HOH . D 4 HOH A 92 452 92 HOH HOH . D 4 HOH A 93 453 93 HOH HOH . D 4 HOH A 94 454 94 HOH HOH . D 4 HOH A 95 455 95 HOH HOH . D 4 HOH A 96 456 96 HOH HOH . D 4 HOH A 97 457 97 HOH HOH . D 4 HOH A 98 458 98 HOH HOH . D 4 HOH A 99 459 99 HOH HOH . D 4 HOH A 100 460 100 HOH HOH . D 4 HOH A 101 461 101 HOH HOH . D 4 HOH A 102 462 102 HOH HOH . D 4 HOH A 103 463 103 HOH HOH . D 4 HOH A 104 464 104 HOH HOH . D 4 HOH A 105 465 105 HOH HOH . D 4 HOH A 106 466 106 HOH HOH . D 4 HOH A 107 467 107 HOH HOH . D 4 HOH A 108 468 108 HOH HOH . D 4 HOH A 109 469 109 HOH HOH . D 4 HOH A 110 470 110 HOH HOH . D 4 HOH A 111 471 111 HOH HOH . D 4 HOH A 112 472 112 HOH HOH . D 4 HOH A 113 473 113 HOH HOH . D 4 HOH A 114 474 114 HOH HOH . D 4 HOH A 115 475 115 HOH HOH . D 4 HOH A 116 476 116 HOH HOH . D 4 HOH A 117 477 117 HOH HOH . D 4 HOH A 118 478 118 HOH HOH . D 4 HOH A 119 479 119 HOH HOH . D 4 HOH A 120 480 120 HOH HOH . D 4 HOH A 121 481 121 HOH HOH . D 4 HOH A 122 482 122 HOH HOH . D 4 HOH A 123 483 123 HOH HOH . D 4 HOH A 124 484 124 HOH HOH . D 4 HOH A 125 485 125 HOH HOH . D 4 HOH A 126 486 126 HOH HOH . D 4 HOH A 127 487 127 HOH HOH . D 4 HOH A 128 488 128 HOH HOH . D 4 HOH A 129 489 129 HOH HOH . D 4 HOH A 130 490 130 HOH HOH . D 4 HOH A 131 491 131 HOH HOH . D 4 HOH A 132 492 132 HOH HOH . D 4 HOH A 133 493 133 HOH HOH . D 4 HOH A 134 494 134 HOH HOH . D 4 HOH A 135 495 135 HOH HOH . D 4 HOH A 136 496 136 HOH HOH . D 4 HOH A 137 497 137 HOH HOH . D 4 HOH A 138 498 138 HOH HOH . D 4 HOH A 139 499 139 HOH HOH . D 4 HOH A 140 500 140 HOH HOH . D 4 HOH A 141 501 141 HOH HOH . D 4 HOH A 142 502 142 HOH HOH . D 4 HOH A 143 503 143 HOH HOH . D 4 HOH A 144 504 144 HOH HOH . D 4 HOH A 145 505 145 HOH HOH . D 4 HOH A 146 506 146 HOH HOH . D 4 HOH A 147 507 147 HOH HOH . D 4 HOH A 148 508 148 HOH HOH . D 4 HOH A 149 509 149 HOH HOH . D 4 HOH A 150 510 150 HOH HOH . D 4 HOH A 151 511 151 HOH HOH . D 4 HOH A 152 512 152 HOH HOH . D 4 HOH A 153 513 153 HOH HOH . D 4 HOH A 154 514 154 HOH HOH . D 4 HOH A 155 515 155 HOH HOH . D 4 HOH A 156 516 156 HOH HOH . D 4 HOH A 157 517 157 HOH HOH . D 4 HOH A 158 518 158 HOH HOH . D 4 HOH A 159 519 159 HOH HOH . D 4 HOH A 160 520 160 HOH HOH . D 4 HOH A 161 521 161 HOH HOH . D 4 HOH A 162 522 162 HOH HOH . D 4 HOH A 163 523 163 HOH HOH . D 4 HOH A 164 524 164 HOH HOH . D 4 HOH A 165 525 165 HOH HOH . D 4 HOH A 166 526 166 HOH HOH . D 4 HOH A 167 527 167 HOH HOH . D 4 HOH A 168 528 168 HOH HOH . D 4 HOH A 169 529 169 HOH HOH . D 4 HOH A 170 530 170 HOH HOH . D 4 HOH A 171 531 171 HOH HOH . D 4 HOH A 172 532 172 HOH HOH . D 4 HOH A 173 533 173 HOH HOH . D 4 HOH A 174 534 174 HOH HOH . D 4 HOH A 175 535 175 HOH HOH . D 4 HOH A 176 536 176 HOH HOH . D 4 HOH A 177 537 177 HOH HOH . D 4 HOH A 178 538 178 HOH HOH . D 4 HOH A 179 539 179 HOH HOH . D 4 HOH A 180 540 180 HOH HOH . D 4 HOH A 181 541 181 HOH HOH . D 4 HOH A 182 542 182 HOH HOH . D 4 HOH A 183 543 183 HOH HOH . D 4 HOH A 184 544 184 HOH HOH . D 4 HOH A 185 545 185 HOH HOH . D 4 HOH A 186 546 186 HOH HOH . D 4 HOH A 187 547 187 HOH HOH . D 4 HOH A 188 548 188 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 N PDD . . . C 3 11.997 -3.311 15.024 1 16.55 ? N PDD 350 A 1 HETATM 2 N N1 PDD . . . C 3 16.976 -2.826 16.857 1 12.87 ? N1 PDD 350 A 1 HETATM 3 C C2 PDD . . . C 3 15.908 -3.332 17.626 1 13.39 ? C2 PDD 350 A 1 HETATM 4 C C2A PDD . . . C 3 16.115 -3.671 19.064 1 12.91 ? C2A PDD 350 A 1 HETATM 5 C C3 PDD . . . C 3 14.594 -3.507 16.949 1 14.31 ? C3 PDD 350 A 1 HETATM 6 O O3A PDD . . . C 3 13.464 -3.976 17.519 1 12.74 ? O3A PDD 350 A 1 HETATM 7 C C4 PDD . . . C 3 14.521 -3.119 15.471 1 14.46 ? C4 PDD 350 A 1 HETATM 8 C C4A PDD . . . C 3 13.252 -3.247 14.672 1 14.83 ? C4A PDD 350 A 1 HETATM 9 C C5 PDD . . . C 3 15.691 -2.607 14.779 1 13.69 ? C5 PDD 350 A 1 HETATM 10 C C5A PDD . . . C 3 15.641 -2.221 13.307 1 18.17 ? C5A PDD 350 A 1 HETATM 11 O OP4 PDD . . . C 3 14.781 -1.127 12.936 1 21.63 ? OP4 PDD 350 A 1 HETATM 12 P P PDD . . . C 3 14.322 -0.885 11.632 1 31.18 ? P PDD 350 A 1 HETATM 13 O OP1 PDD . . . C 3 13.389 -2.035 11.354 1 22.45 ? OP1 PDD 350 A 1 HETATM 14 O OP2 PDD . . . C 3 13.551 0.3 11.712 1 22.25 ? OP2 PDD 350 A 1 HETATM 15 O OP3 PDD . . . C 3 15.103 -0.83 10.483 1 22.25 ? OP3 PDD 350 A 1 HETATM 16 C C6 PDD . . . C 3 16.938 -2.464 15.506 1 14.42 ? C6 PDD 350 A 1 HETATM 17 C CA PDD . . . C 3 10.771 -3.43 14.212 1 16.28 ? CA PDD 350 A 1 HETATM 18 C CB PDD . . . C 3 10.383 -2.129 13.566 1 18.76 ? CB PDD 350 A 1 HETATM 19 C C PDD . . . C 3 9.549 -3.869 15.143 1 14.09 ? C PDD 350 A 1 HETATM 20 O O PDD . . . C 3 9.706 -4.039 16.347 1 14.05 ? O PDD 350 A 1 HETATM 21 O OXT PDD . . . C 3 8.41 -4.047 14.68 1 13.26 ? OXT PDD 350 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #