data_8PNY # _model_server_result.job_id el0BXEimeLOOE9F-v-4yUw _model_server_result.datetime_utc '2024-11-24 19:06:59' _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 8pny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 8PNY # _exptl.entry_id 8PNY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 337.268 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[6-methyl-5-oxidanyl-4-[(2-phenylhydrazinyl)methyl]pyridin-3-yl]methyl dihydrogen 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 120 _cell.entry_id 8PNY _cell.length_a 104.644 _cell.length_b 104.644 _cell.length_c 51.541 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PNY _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 _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' 5_553 x-y,-y,-z-4/3 1 0 0 0 -1 0 0 0 -1 0 0 -68.721333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C14 H16 N3 O5 P' _chem_comp.formula_weight 337.268 _chem_comp.id ZXN _chem_comp.mon_nstd_flag . _chem_comp.name '[6-methyl-5-oxidanyl-4-[(2-phenylhydrazinyl)methyl]pyridin-3-yl]methyl dihydrogen phosphate' _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 CE2 CZ ZXN doub 376 n y CE2 CD2 ZXN sing 377 n y CZ CE1 ZXN sing 378 n y CD2 CG ZXN doub 379 n y C2A C2 ZXN sing 380 n n CE1 CD1 ZXN doub 381 n y O3 C3 ZXN sing 382 n n CG CD1 ZXN sing 383 n y CG N' ZXN sing 384 n n C2 C3 ZXN doub 385 n y C2 N1 ZXN sing 386 n y C3 C4 ZXN sing 387 n y N N' ZXN sing 388 n n N C4A ZXN doub 389 e n N1 C6 ZXN doub 390 n y C4A C4 ZXN sing 391 n n C4 C5 ZXN doub 392 n y C6 C5 ZXN sing 393 n y C5 C5A ZXN sing 394 n n C5A O4P ZXN sing 395 n n O4P P ZXN sing 396 n n O1P P ZXN doub 397 n n P O2P ZXN sing 398 n n P O3P ZXN sing 399 n n C6 H2 ZXN sing 400 n n C2A H3 ZXN sing 401 n n C2A H4 ZXN sing 402 n n C2A H5 ZXN sing 403 n n O3 H6 ZXN sing 404 n n C4A H7 ZXN sing 405 n n C5A H9 ZXN sing 406 n n C5A H10 ZXN sing 407 n n O2P H11 ZXN sing 408 n n O3P H12 ZXN sing 409 n n N' H13 ZXN sing 410 n n CD2 H14 ZXN sing 411 n n CE2 H15 ZXN sing 412 n n CZ H16 ZXN sing 413 n n CE1 H17 ZXN sing 414 n n CD1 H18 ZXN sing 415 n n # _atom_sites.entry_id 8PNY _atom_sites.fract_transf_matrix[1][1] 0.009556 _atom_sites.fract_transf_matrix[1][2] 0.005517 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011035 _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] 0.019402 _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 ZXN A 1 301 301 ZXN 00O . C 3 HOH A 1 401 215 HOH HOH . C 3 HOH A 2 402 230 HOH HOH . C 3 HOH A 3 403 76 HOH HOH . C 3 HOH A 4 404 199 HOH HOH . C 3 HOH A 5 405 197 HOH HOH . C 3 HOH A 6 406 2 HOH HOH . C 3 HOH A 7 407 15 HOH HOH . C 3 HOH A 8 408 127 HOH HOH . C 3 HOH A 9 409 125 HOH HOH . C 3 HOH A 10 410 97 HOH HOH . C 3 HOH A 11 411 224 HOH HOH . C 3 HOH A 12 412 42 HOH HOH . C 3 HOH A 13 413 101 HOH HOH . C 3 HOH A 14 414 32 HOH HOH . C 3 HOH A 15 415 151 HOH HOH . C 3 HOH A 16 416 100 HOH HOH . C 3 HOH A 17 417 109 HOH HOH . C 3 HOH A 18 418 6 HOH HOH . C 3 HOH A 19 419 70 HOH HOH . C 3 HOH A 20 420 11 HOH HOH . C 3 HOH A 21 421 39 HOH HOH . C 3 HOH A 22 422 58 HOH HOH . C 3 HOH A 23 423 124 HOH HOH . C 3 HOH A 24 424 159 HOH HOH . C 3 HOH A 25 425 150 HOH HOH . C 3 HOH A 26 426 45 HOH HOH . C 3 HOH A 27 427 80 HOH HOH . C 3 HOH A 28 428 200 HOH HOH . C 3 HOH A 29 429 156 HOH HOH . C 3 HOH A 30 430 111 HOH HOH . C 3 HOH A 31 431 139 HOH HOH . C 3 HOH A 32 432 167 HOH HOH . C 3 HOH A 33 433 155 HOH HOH . C 3 HOH A 34 434 67 HOH HOH . C 3 HOH A 35 435 117 HOH HOH . C 3 HOH A 36 436 84 HOH HOH . C 3 HOH A 37 437 120 HOH HOH . C 3 HOH A 38 438 234 HOH HOH . C 3 HOH A 39 439 61 HOH HOH . C 3 HOH A 40 440 145 HOH HOH . C 3 HOH A 41 441 56 HOH HOH . C 3 HOH A 42 442 211 HOH HOH . C 3 HOH A 43 443 133 HOH HOH . C 3 HOH A 44 444 178 HOH HOH . C 3 HOH A 45 445 83 HOH HOH . C 3 HOH A 46 446 214 HOH HOH . C 3 HOH A 47 447 108 HOH HOH . C 3 HOH A 48 448 77 HOH HOH . C 3 HOH A 49 449 65 HOH HOH . C 3 HOH A 50 450 172 HOH HOH . C 3 HOH A 51 451 229 HOH HOH . C 3 HOH A 52 452 216 HOH HOH . C 3 HOH A 53 453 136 HOH HOH . C 3 HOH A 54 454 33 HOH HOH . C 3 HOH A 55 455 21 HOH HOH . C 3 HOH A 56 456 185 HOH HOH . C 3 HOH A 57 457 54 HOH HOH . C 3 HOH A 58 458 40 HOH HOH . C 3 HOH A 59 459 115 HOH HOH . C 3 HOH A 60 460 46 HOH HOH . C 3 HOH A 61 461 128 HOH HOH . C 3 HOH A 62 462 161 HOH HOH . C 3 HOH A 63 463 226 HOH HOH . C 3 HOH A 64 464 57 HOH HOH . C 3 HOH A 65 465 29 HOH HOH . C 3 HOH A 66 466 237 HOH HOH . C 3 HOH A 67 467 24 HOH HOH . C 3 HOH A 68 468 12 HOH HOH . C 3 HOH A 69 469 148 HOH HOH . C 3 HOH A 70 470 55 HOH HOH . C 3 HOH A 71 471 74 HOH HOH . C 3 HOH A 72 472 131 HOH HOH . C 3 HOH A 73 473 201 HOH HOH . C 3 HOH A 74 474 9 HOH HOH . C 3 HOH A 75 475 179 HOH HOH . C 3 HOH A 76 476 79 HOH HOH . C 3 HOH A 77 477 16 HOH HOH . C 3 HOH A 78 478 142 HOH HOH . C 3 HOH A 79 479 93 HOH HOH . C 3 HOH A 80 480 192 HOH HOH . C 3 HOH A 81 481 189 HOH HOH . C 3 HOH A 82 482 22 HOH HOH . C 3 HOH A 83 483 81 HOH HOH . C 3 HOH A 84 484 99 HOH HOH . C 3 HOH A 85 485 222 HOH HOH . C 3 HOH A 86 486 235 HOH HOH . C 3 HOH A 87 487 212 HOH HOH . C 3 HOH A 88 488 4 HOH HOH . C 3 HOH A 89 489 60 HOH HOH . C 3 HOH A 90 490 27 HOH HOH . C 3 HOH A 91 491 107 HOH HOH . C 3 HOH A 92 492 44 HOH HOH . C 3 HOH A 93 493 106 HOH HOH . C 3 HOH A 94 494 50 HOH HOH . C 3 HOH A 95 495 20 HOH HOH . C 3 HOH A 96 496 47 HOH HOH . C 3 HOH A 97 497 181 HOH HOH . C 3 HOH A 98 498 110 HOH HOH . C 3 HOH A 99 499 112 HOH HOH . C 3 HOH A 100 500 71 HOH HOH . C 3 HOH A 101 501 28 HOH HOH . C 3 HOH A 102 502 220 HOH HOH . C 3 HOH A 103 503 149 HOH HOH . C 3 HOH A 104 504 3 HOH HOH . C 3 HOH A 105 505 186 HOH HOH . C 3 HOH A 106 506 206 HOH HOH . C 3 HOH A 107 507 104 HOH HOH . C 3 HOH A 108 508 36 HOH HOH . C 3 HOH A 109 509 138 HOH HOH . C 3 HOH A 110 510 53 HOH HOH . C 3 HOH A 111 511 14 HOH HOH . C 3 HOH A 112 512 10 HOH HOH . C 3 HOH A 113 513 87 HOH HOH . C 3 HOH A 114 514 137 HOH HOH . C 3 HOH A 115 515 31 HOH HOH . C 3 HOH A 116 516 146 HOH HOH . C 3 HOH A 117 517 175 HOH HOH . C 3 HOH A 118 518 183 HOH HOH . C 3 HOH A 119 519 114 HOH HOH . C 3 HOH A 120 520 195 HOH HOH . C 3 HOH A 121 521 52 HOH HOH . C 3 HOH A 122 522 184 HOH HOH . C 3 HOH A 123 523 38 HOH HOH . C 3 HOH A 124 524 19 HOH HOH . C 3 HOH A 125 525 98 HOH HOH . C 3 HOH A 126 526 168 HOH HOH . C 3 HOH A 127 527 190 HOH HOH . C 3 HOH A 128 528 209 HOH HOH . C 3 HOH A 129 529 140 HOH HOH . C 3 HOH A 130 530 129 HOH HOH . C 3 HOH A 131 531 154 HOH HOH . C 3 HOH A 132 532 213 HOH HOH . C 3 HOH A 133 533 82 HOH HOH . C 3 HOH A 134 534 233 HOH HOH . C 3 HOH A 135 535 86 HOH HOH . C 3 HOH A 136 536 163 HOH HOH . C 3 HOH A 137 537 169 HOH HOH . C 3 HOH A 138 538 170 HOH HOH . C 3 HOH A 139 539 66 HOH HOH . C 3 HOH A 140 540 121 HOH HOH . C 3 HOH A 141 541 41 HOH HOH . C 3 HOH A 142 542 91 HOH HOH . C 3 HOH A 143 543 92 HOH HOH . C 3 HOH A 144 544 68 HOH HOH . C 3 HOH A 145 545 203 HOH HOH . C 3 HOH A 146 546 135 HOH HOH . C 3 HOH A 147 547 231 HOH HOH . C 3 HOH A 148 548 171 HOH HOH . C 3 HOH A 149 549 119 HOH HOH . C 3 HOH A 150 550 8 HOH HOH . C 3 HOH A 151 551 89 HOH HOH . C 3 HOH A 152 552 202 HOH HOH . C 3 HOH A 153 553 75 HOH HOH . C 3 HOH A 154 554 152 HOH HOH . C 3 HOH A 155 555 236 HOH HOH . C 3 HOH A 156 556 144 HOH HOH . C 3 HOH A 157 557 116 HOH HOH . C 3 HOH A 158 558 78 HOH HOH . C 3 HOH A 159 559 210 HOH HOH . C 3 HOH A 160 560 196 HOH HOH . C 3 HOH A 161 561 85 HOH HOH . C 3 HOH A 162 562 132 HOH HOH . C 3 HOH A 163 563 204 HOH HOH . C 3 HOH A 164 564 72 HOH HOH . C 3 HOH A 165 565 158 HOH HOH . C 3 HOH A 166 566 59 HOH HOH . C 3 HOH A 167 567 96 HOH HOH . C 3 HOH A 168 568 113 HOH HOH . C 3 HOH A 169 569 123 HOH HOH . C 3 HOH A 170 570 177 HOH HOH . C 3 HOH A 171 571 217 HOH HOH . C 3 HOH A 172 572 94 HOH HOH . C 3 HOH A 173 573 48 HOH HOH . C 3 HOH A 174 574 5 HOH HOH . C 3 HOH A 175 575 223 HOH HOH . C 3 HOH A 176 576 1 HOH HOH . C 3 HOH A 177 577 176 HOH HOH . C 3 HOH A 178 578 118 HOH HOH . C 3 HOH A 179 579 187 HOH HOH . C 3 HOH A 180 580 221 HOH HOH . C 3 HOH A 181 581 238 HOH HOH . C 3 HOH A 182 582 13 HOH HOH . C 3 HOH A 183 583 105 HOH HOH . C 3 HOH A 184 584 7 HOH HOH . C 3 HOH A 185 585 141 HOH HOH . C 3 HOH A 186 586 143 HOH HOH . C 3 HOH A 187 587 95 HOH HOH . C 3 HOH A 188 588 153 HOH HOH . C 3 HOH A 189 589 51 HOH HOH . C 3 HOH A 190 590 160 HOH HOH . C 3 HOH A 191 591 35 HOH HOH . C 3 HOH A 192 592 219 HOH HOH . C 3 HOH A 193 593 17 HOH HOH . C 3 HOH A 194 594 208 HOH HOH . C 3 HOH A 195 595 191 HOH HOH . C 3 HOH A 196 596 173 HOH HOH . C 3 HOH A 197 597 63 HOH HOH . C 3 HOH A 198 598 26 HOH HOH . C 3 HOH A 199 599 25 HOH HOH . C 3 HOH A 200 600 37 HOH HOH . C 3 HOH A 201 601 227 HOH HOH . C 3 HOH A 202 602 205 HOH HOH . C 3 HOH A 203 603 30 HOH HOH . C 3 HOH A 204 604 73 HOH HOH . C 3 HOH A 205 605 165 HOH HOH . C 3 HOH A 206 606 182 HOH HOH . C 3 HOH A 207 607 232 HOH HOH . C 3 HOH A 208 608 23 HOH HOH . C 3 HOH A 209 609 228 HOH HOH . C 3 HOH A 210 610 130 HOH HOH . C 3 HOH A 211 611 90 HOH HOH . C 3 HOH A 212 612 126 HOH HOH . C 3 HOH A 213 613 174 HOH HOH . C 3 HOH A 214 614 43 HOH HOH . C 3 HOH A 215 615 225 HOH HOH . C 3 HOH A 216 616 198 HOH HOH . C 3 HOH A 217 617 134 HOH HOH . C 3 HOH A 218 618 88 HOH HOH . C 3 HOH A 219 619 207 HOH HOH . C 3 HOH A 220 620 34 HOH HOH . C 3 HOH A 221 621 193 HOH HOH . C 3 HOH A 222 622 164 HOH HOH . C 3 HOH A 223 623 62 HOH HOH . C 3 HOH A 224 624 64 HOH HOH . C 3 HOH A 225 625 218 HOH HOH . C 3 HOH A 226 626 194 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 ZXN . A . B 2 -47.963 7.217 -22.422 0.5 24.26 ? N ZXN 301 A 1 HETATM 2 C C6 ZXN . A . B 2 -52.481 7.381 -21.287 0.5 18.41 ? C6 ZXN 301 A 1 HETATM 3 C C5 ZXN . A . B 2 -51.246 7.845 -20.894 0.5 18.36 ? C5 ZXN 301 A 1 HETATM 4 C C4 ZXN . A . B 2 -50.311 7.507 -21.941 0.5 18.54 ? C4 ZXN 301 A 1 HETATM 5 C C3 ZXN . A . B 2 -50.716 6.858 -23.161 0.5 18.6 ? C3 ZXN 301 A 1 HETATM 6 C C2 ZXN . A . B 2 -52.043 6.5 -23.348 0.5 18.47 ? C2 ZXN 301 A 1 HETATM 7 N N1 ZXN . A . B 2 -52.894 6.756 -22.395 0.5 19.53 ? N1 ZXN 301 A 1 HETATM 8 C C2A ZXN . A . B 2 -52.58 5.793 -24.543 0.5 18.49 ? C2A ZXN 301 A 1 HETATM 9 O O3 ZXN . A . B 2 -49.667 6.679 -24.015 0.5 17.2 ? O3 ZXN 301 A 1 HETATM 10 C C4A ZXN . A . B 2 -48.919 7.912 -21.942 0.5 20.91 ? C4A ZXN 301 A 1 HETATM 11 C C5A ZXN . A . B 2 -51.397 8.437 -19.526 0.5 17.54 ? C5A ZXN 301 A 1 HETATM 12 O O4P ZXN . A . B 2 -50.371 7.856 -18.654 0.5 15.27 ? O4P ZXN 301 A 1 HETATM 13 P P ZXN . A . B 2 -49.262 8.315 -17.545 0.5 13.63 ? P ZXN 301 A 1 HETATM 14 O O1P ZXN . A . B 2 -48.193 8.961 -18.369 0.5 12.8 ? O1P ZXN 301 A 1 HETATM 15 O O2P ZXN . A . B 2 -48.709 7.086 -16.833 0.5 14.75 ? O2P ZXN 301 A 1 HETATM 16 O O3P ZXN . A . B 2 -49.996 9.252 -16.582 0.5 12.76 ? O3P ZXN 301 A 1 HETATM 17 N N' ZXN . A . B 2 -46.728 7.784 -22.268 0.5 26.81 ? N' ZXN 301 A 1 HETATM 18 C CG ZXN . A . B 2 -46.065 8.293 -23.38 0.5 28.62 ? CG ZXN 301 A 1 HETATM 19 C CD2 ZXN . A . B 2 -46.622 8.087 -24.636 0.5 29.26 ? CD2 ZXN 301 A 1 HETATM 20 C CE2 ZXN . A . B 2 -45.97 8.568 -25.756 0.5 29.16 ? CE2 ZXN 301 A 1 HETATM 21 C CZ ZXN . A . B 2 -44.784 9.251 -25.634 0.5 29.48 ? CZ ZXN 301 A 1 HETATM 22 C CE1 ZXN . A . B 2 -44.232 9.46 -24.395 0.5 29.15 ? CE1 ZXN 301 A 1 HETATM 23 C CD1 ZXN . A . B 2 -44.871 8.993 -23.259 0.5 28.92 ? CD1 ZXN 301 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 23 #