data_3V1U # _model_server_result.job_id kdw0NXl5nNO-aHAT7ym7JA _model_server_result.datetime_utc '2024-12-01 20:56:50' _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 3v1u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3V1U # _exptl.entry_id 3V1U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 3V1U _cell.length_a 103.059 _cell.length_b 103.059 _cell.length_c 76.047 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V1U _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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,E _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_554 x-y,-y,-z-2/3 1 0 0 0 -1 0 0 0 -1 0 0 -50.698 # _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 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 PA O1A NAD doub 340 n n PA O2A NAD sing 341 n n PA O5B NAD sing 342 n n PA O3 NAD sing 343 n n O2A HOA2 NAD sing 344 n n O5B C5B NAD sing 345 n n C5B C4B NAD sing 346 n n C5B H51A NAD sing 347 n n C5B H52A NAD sing 348 n n C4B O4B NAD sing 349 n n C4B C3B NAD sing 350 n n C4B H4B NAD sing 351 n n O4B C1B NAD sing 352 n n C3B O3B NAD sing 353 n n C3B C2B NAD sing 354 n n C3B H3B NAD sing 355 n n O3B HO3A NAD sing 356 n n C2B O2B NAD sing 357 n n C2B C1B NAD sing 358 n n C2B H2B NAD sing 359 n n O2B HO2A NAD sing 360 n n C1B N9A NAD sing 361 n n C1B H1B NAD sing 362 n n N9A C8A NAD sing 363 n y N9A C4A NAD sing 364 n y C8A N7A NAD doub 365 n y C8A H8A NAD sing 366 n n N7A C5A NAD sing 367 n y C5A C6A NAD sing 368 n y C5A C4A NAD doub 369 n y C6A N6A NAD sing 370 n n C6A N1A NAD doub 371 n y N6A H61A NAD sing 372 n n N6A H62A NAD sing 373 n n N1A C2A NAD sing 374 n y C2A N3A NAD doub 375 n y C2A H2A NAD sing 376 n n N3A C4A NAD sing 377 n y O3 PN NAD sing 378 n n PN O1N NAD doub 379 n n PN O2N NAD sing 380 n n PN O5D NAD sing 381 n n O5D C5D NAD sing 382 n n C5D C4D NAD sing 383 n n C5D H51N NAD sing 384 n n C5D H52N NAD sing 385 n n C4D O4D NAD sing 386 n n C4D C3D NAD sing 387 n n C4D H4D NAD sing 388 n n O4D C1D NAD sing 389 n n C3D O3D NAD sing 390 n n C3D C2D NAD sing 391 n n C3D H3D NAD sing 392 n n O3D HO3N NAD sing 393 n n C2D O2D NAD sing 394 n n C2D C1D NAD sing 395 n n C2D H2D NAD sing 396 n n O2D HO2N NAD sing 397 n n C1D N1N NAD sing 398 n n C1D H1D NAD sing 399 n n N1N C2N NAD sing 400 n y N1N C6N NAD doub 401 n y C2N C3N NAD doub 402 n y C2N H2N NAD sing 403 n n C3N C7N NAD sing 404 n n C3N C4N NAD sing 405 n y C7N O7N NAD doub 406 n n C7N N7N NAD sing 407 n n N7N H71N NAD sing 408 n n N7N H72N NAD sing 409 n n C4N C5N NAD doub 410 n y C4N H4N NAD sing 411 n n C5N C6N NAD sing 412 n y C5N H5N NAD sing 413 n n C6N H6N NAD sing 414 n n # _atom_sites.entry_id 3V1U _atom_sites.fract_transf_matrix[1][1] 0.009703 _atom_sites.fract_transf_matrix[1][2] 0.005602 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011204 _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] 0.01315 _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 NAD A 1 501 457 NAD NAD . C 3 HXC A 1 502 1 HXC HXC . D 4 ZPG A 1 503 1 ZPG POG . E 5 HOH A 1 601 458 HOH HOH . E 5 HOH A 2 602 459 HOH HOH . E 5 HOH A 3 603 460 HOH HOH . E 5 HOH A 4 604 461 HOH HOH . E 5 HOH A 5 605 462 HOH HOH . E 5 HOH A 6 606 463 HOH HOH . E 5 HOH A 7 607 464 HOH HOH . E 5 HOH A 8 608 465 HOH HOH . E 5 HOH A 9 609 466 HOH HOH . E 5 HOH A 10 610 467 HOH HOH . E 5 HOH A 11 611 468 HOH HOH . E 5 HOH A 12 612 469 HOH HOH . E 5 HOH A 13 613 470 HOH HOH . E 5 HOH A 14 614 471 HOH HOH . E 5 HOH A 15 615 472 HOH HOH . E 5 HOH A 16 616 473 HOH HOH . E 5 HOH A 17 617 474 HOH HOH . E 5 HOH A 18 618 475 HOH HOH . E 5 HOH A 19 619 476 HOH HOH . E 5 HOH A 20 620 477 HOH HOH . E 5 HOH A 21 621 478 HOH HOH . E 5 HOH A 22 622 479 HOH HOH . E 5 HOH A 23 623 480 HOH HOH . E 5 HOH A 24 624 481 HOH HOH . E 5 HOH A 25 625 482 HOH HOH . E 5 HOH A 26 626 483 HOH HOH . E 5 HOH A 27 627 484 HOH HOH . E 5 HOH A 28 628 485 HOH HOH . E 5 HOH A 29 629 486 HOH HOH . E 5 HOH A 30 630 487 HOH HOH . E 5 HOH A 31 631 488 HOH HOH . E 5 HOH A 32 632 489 HOH HOH . E 5 HOH A 33 633 490 HOH HOH . E 5 HOH A 34 634 491 HOH HOH . E 5 HOH A 35 635 492 HOH HOH . E 5 HOH A 36 636 493 HOH HOH . E 5 HOH A 37 637 494 HOH HOH . E 5 HOH A 38 638 495 HOH HOH . E 5 HOH A 39 639 496 HOH HOH . E 5 HOH A 40 640 497 HOH HOH . E 5 HOH A 41 641 498 HOH HOH . E 5 HOH A 42 642 499 HOH HOH . E 5 HOH A 43 643 500 HOH HOH . E 5 HOH A 44 644 501 HOH HOH . E 5 HOH A 45 645 502 HOH HOH . E 5 HOH A 46 646 503 HOH HOH . E 5 HOH A 47 647 504 HOH HOH . E 5 HOH A 48 648 505 HOH HOH . E 5 HOH A 49 649 506 HOH HOH . E 5 HOH A 50 650 507 HOH HOH . E 5 HOH A 51 651 508 HOH HOH . E 5 HOH A 52 652 509 HOH HOH . E 5 HOH A 53 653 510 HOH HOH . E 5 HOH A 54 654 511 HOH HOH . E 5 HOH A 55 655 512 HOH HOH . E 5 HOH A 56 656 513 HOH HOH . E 5 HOH A 57 657 514 HOH HOH . E 5 HOH A 58 658 515 HOH HOH . E 5 HOH A 59 659 516 HOH HOH . E 5 HOH A 60 660 517 HOH HOH . E 5 HOH A 61 661 518 HOH HOH . E 5 HOH A 62 662 519 HOH HOH . E 5 HOH A 63 663 520 HOH HOH . E 5 HOH A 64 664 521 HOH HOH . E 5 HOH A 65 665 522 HOH HOH . E 5 HOH A 66 666 523 HOH HOH . E 5 HOH A 67 667 524 HOH HOH . E 5 HOH A 68 668 525 HOH HOH . E 5 HOH A 69 669 526 HOH HOH . E 5 HOH A 70 670 527 HOH HOH . E 5 HOH A 71 671 528 HOH HOH . E 5 HOH A 72 672 529 HOH HOH . E 5 HOH A 73 673 530 HOH HOH . E 5 HOH A 74 674 531 HOH HOH . E 5 HOH A 75 675 532 HOH HOH . E 5 HOH A 76 676 533 HOH HOH . E 5 HOH A 77 677 534 HOH HOH . E 5 HOH A 78 678 535 HOH HOH . E 5 HOH A 79 679 536 HOH HOH . E 5 HOH A 80 680 537 HOH HOH . E 5 HOH A 81 681 538 HOH HOH . E 5 HOH A 82 682 539 HOH HOH . E 5 HOH A 83 683 540 HOH HOH . E 5 HOH A 84 684 541 HOH HOH . E 5 HOH A 85 685 542 HOH HOH . E 5 HOH A 86 686 543 HOH HOH . E 5 HOH A 87 687 544 HOH HOH . E 5 HOH A 88 688 545 HOH HOH . E 5 HOH A 89 689 546 HOH HOH . E 5 HOH A 90 690 547 HOH HOH . E 5 HOH A 91 691 548 HOH HOH . E 5 HOH A 92 692 549 HOH HOH . E 5 HOH A 93 693 550 HOH HOH . E 5 HOH A 94 694 551 HOH HOH . E 5 HOH A 95 695 552 HOH HOH . E 5 HOH A 96 696 553 HOH HOH . E 5 HOH A 97 697 554 HOH HOH . E 5 HOH A 98 698 555 HOH HOH . E 5 HOH A 99 699 556 HOH HOH . E 5 HOH A 100 700 557 HOH HOH . E 5 HOH A 101 701 558 HOH HOH . E 5 HOH A 102 702 559 HOH HOH . E 5 HOH A 103 703 560 HOH HOH . E 5 HOH A 104 704 561 HOH HOH . E 5 HOH A 105 705 562 HOH HOH . E 5 HOH A 106 706 563 HOH HOH . E 5 HOH A 107 707 564 HOH HOH . E 5 HOH A 108 708 565 HOH HOH . E 5 HOH A 109 709 566 HOH HOH . E 5 HOH A 110 710 567 HOH HOH . E 5 HOH A 111 711 568 HOH HOH . E 5 HOH A 112 712 569 HOH HOH . E 5 HOH A 113 713 570 HOH HOH . E 5 HOH A 114 714 571 HOH HOH . E 5 HOH A 115 715 572 HOH HOH . E 5 HOH A 116 716 573 HOH HOH . E 5 HOH A 117 717 574 HOH HOH . E 5 HOH A 118 718 575 HOH HOH . E 5 HOH A 119 719 576 HOH HOH . E 5 HOH A 120 720 1 HOH HOH . E 5 HOH A 121 721 2 HOH HOH . E 5 HOH A 122 722 3 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 P PA NAD . . . B 2 48.539 -23.036 -18.085 1 43.96 ? PA NAD 501 A 1 HETATM 2 O O1A NAD . . . B 2 48.792 -23.706 -19.47 1 42.05 ? O1A NAD 501 A 1 HETATM 3 O O2A NAD . . . B 2 49.644 -23.279 -17.082 1 44.23 ? O2A NAD 501 A 1 HETATM 4 O O5B NAD . . . B 2 47.17 -23.562 -17.402 1 43.73 ? O5B NAD 501 A 1 HETATM 5 C C5B NAD . . . B 2 46.108 -24.12 -18.158 1 44.55 ? C5B NAD 501 A 1 HETATM 6 C C4B NAD . . . B 2 45.64 -25.447 -17.673 1 46.21 ? C4B NAD 501 A 1 HETATM 7 O O4B NAD . . . B 2 44.459 -25.745 -18.475 1 44.89 ? O4B NAD 501 A 1 HETATM 8 C C3B NAD . . . B 2 46.595 -26.541 -17.839 1 43.53 ? C3B NAD 501 A 1 HETATM 9 O O3B NAD . . . B 2 46.7 -27.335 -16.667 1 37.42 ? O3B NAD 501 A 1 HETATM 10 C C2B NAD . . . B 2 45.977 -27.394 -18.88 1 42.96 ? C2B NAD 501 A 1 HETATM 11 O O2B NAD . . . B 2 46.236 -28.737 -18.581 1 41.24 ? O2B NAD 501 A 1 HETATM 12 C C1B NAD . . . B 2 44.544 -27.109 -18.709 1 41.57 ? C1B NAD 501 A 1 HETATM 13 N N9A NAD . . . B 2 43.794 -27.449 -19.912 1 36.02 ? N9A NAD 501 A 1 HETATM 14 C C8A NAD . . . B 2 44.176 -27.138 -21.134 1 35.73 ? C8A NAD 501 A 1 HETATM 15 N N7A NAD . . . B 2 43.268 -27.635 -21.99 1 37.79 ? N7A NAD 501 A 1 HETATM 16 C C5A NAD . . . B 2 42.312 -28.253 -21.261 1 35.24 ? C5A NAD 501 A 1 HETATM 17 C C6A NAD . . . B 2 41.15 -28.965 -21.579 1 35.45 ? C6A NAD 501 A 1 HETATM 18 N N6A NAD . . . B 2 40.781 -29.082 -22.926 1 36.26 ? N6A NAD 501 A 1 HETATM 19 N N1A NAD . . . B 2 40.376 -29.486 -20.589 1 35.67 ? N1A NAD 501 A 1 HETATM 20 C C2A NAD . . . B 2 40.726 -29.364 -19.283 1 35.48 ? C2A NAD 501 A 1 HETATM 21 N N3A NAD . . . B 2 41.855 -28.703 -18.976 1 35.38 ? N3A NAD 501 A 1 HETATM 22 C C4A NAD . . . B 2 42.647 -28.141 -19.928 1 34.52 ? C4A NAD 501 A 1 HETATM 23 O O3 NAD . . . B 2 48.35 -21.512 -18.384 1 45.88 ? O3 NAD 501 A 1 HETATM 24 P PN NAD . . . B 2 47.838 -20.396 -17.43 1 45.59 ? PN NAD 501 A 1 HETATM 25 O O1N NAD . . . B 2 48.946 -19.333 -17.501 1 48.82 ? O1N NAD 501 A 1 HETATM 26 O O2N NAD . . . B 2 47.548 -20.775 -16 1 40.59 ? O2N NAD 501 A 1 HETATM 27 O O5D NAD . . . B 2 46.567 -19.782 -18.171 1 47.51 ? O5D NAD 501 A 1 HETATM 28 C C5D NAD . . . B 2 45.36 -19.6 -17.518 1 48.7 ? C5D NAD 501 A 1 HETATM 29 C C4D NAD . . . B 2 44.225 -18.909 -18.192 1 48.38 ? C4D NAD 501 A 1 HETATM 30 O O4D NAD . . . B 2 44.385 -17.493 -18.23 1 49.21 ? O4D NAD 501 A 1 HETATM 31 C C3D NAD . . . B 2 44.122 -19.333 -19.584 1 48.95 ? C3D NAD 501 A 1 HETATM 32 O O3D NAD . . . B 2 42.761 -19.378 -19.959 1 44.72 ? O3D NAD 501 A 1 HETATM 33 C C2D NAD . . . B 2 44.819 -18.333 -20.317 1 50.25 ? C2D NAD 501 A 1 HETATM 34 O O2D NAD . . . B 2 44.388 -18.321 -21.616 1 49.1 ? O2D NAD 501 A 1 HETATM 35 C C1D NAD . . . B 2 44.525 -17.094 -19.546 1 53.79 ? C1D NAD 501 A 1 HETATM 36 N N1N NAD . . . B 2 45.571 -16.042 -19.687 1 61.31 ? N1N NAD 501 A 1 HETATM 37 C C2N NAD . . . B 2 46.826 -16.287 -19.293 1 65.3 ? C2N NAD 501 A 1 HETATM 38 C C3N NAD . . . B 2 47.839 -15.316 -19.419 1 69.18 ? C3N NAD 501 A 1 HETATM 39 C C7N NAD . . . B 2 49.236 -15.678 -19.007 1 70.29 ? C7N NAD 501 A 1 HETATM 40 O O7N NAD . . . B 2 49.247 -16.769 -18.154 1 71.42 ? O7N NAD 501 A 1 HETATM 41 N N7N NAD . . . B 2 50.029 -14.511 -18.57 1 71.89 ? N7N NAD 501 A 1 HETATM 42 C C4N NAD . . . B 2 47.547 -14.05 -19.981 1 67.96 ? C4N NAD 501 A 1 HETATM 43 C C5N NAD . . . B 2 46.237 -13.82 -20.378 1 66.85 ? C5N NAD 501 A 1 HETATM 44 C C6N NAD . . . B 2 45.262 -14.834 -20.224 1 65.77 ? C6N NAD 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 44 #