data_7N46 # _model_server_result.job_id Q1vYSss_SI1V63aOoHk6dQ _model_server_result.datetime_utc '2025-07-07 19:19:45' _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 7n46 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7N46 # _exptl.entry_id 7N46 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 7N46 _cell.length_a 101.646 _cell.length_b 101.646 _cell.length_c 153.444 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7N46 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # 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 metalc ? metalc1 B O2B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc2 D MG MG . A MG 403 1_555 E O3 PO4 . A PO4 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc3 D MG MG . A MG 403 1_555 F O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc4 D MG MG . A MG 403 1_555 F O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.888 ? metalc ? metalc5 D MG MG . A MG 403 1_555 F O HOH . A HOH 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc6 D MG MG . A MG 403 1_555 F O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 7N46 _atom_sites.fract_transf_matrix[1][1] 0.009838 _atom_sites.fract_transf_matrix[1][2] 0.00568 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01136 _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] 0.006517 _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 ADP A 1 401 384 ADP ADP . C 3 NO3 A 1 402 387 NO3 NO3 . D 4 MG A 1 403 601 MG MG . E 5 PO4 A 1 404 1101 PO4 PO4 . F 6 HOH A 1 501 515 HOH HOH . F 6 HOH A 2 502 801 HOH HOH . F 6 HOH A 3 503 701 HOH HOH . F 6 HOH A 4 504 491 HOH HOH . F 6 HOH A 5 505 580 HOH HOH . F 6 HOH A 6 506 478 HOH HOH . F 6 HOH A 7 507 444 HOH HOH . F 6 HOH A 8 508 521 HOH HOH . F 6 HOH A 9 509 537 HOH HOH . F 6 HOH A 10 510 461 HOH HOH . F 6 HOH A 11 511 514 HOH HOH . F 6 HOH A 12 512 417 HOH HOH . F 6 HOH A 13 513 475 HOH HOH . F 6 HOH A 14 514 575 HOH HOH . F 6 HOH A 15 515 456 HOH HOH . F 6 HOH A 16 516 431 HOH HOH . F 6 HOH A 17 517 470 HOH HOH . F 6 HOH A 18 518 553 HOH HOH . F 6 HOH A 19 519 525 HOH HOH . F 6 HOH A 20 520 398 HOH HOH . F 6 HOH A 21 521 445 HOH HOH . F 6 HOH A 22 522 523 HOH HOH . F 6 HOH A 23 523 573 HOH HOH . F 6 HOH A 24 524 510 HOH HOH . F 6 HOH A 25 525 453 HOH HOH . F 6 HOH A 26 526 416 HOH HOH . F 6 HOH A 27 527 448 HOH HOH . F 6 HOH A 28 528 487 HOH HOH . F 6 HOH A 29 529 432 HOH HOH . F 6 HOH A 30 530 467 HOH HOH . F 6 HOH A 31 531 409 HOH HOH . F 6 HOH A 32 532 558 HOH HOH . F 6 HOH A 33 533 439 HOH HOH . F 6 HOH A 34 534 464 HOH HOH . F 6 HOH A 35 535 528 HOH HOH . F 6 HOH A 36 536 389 HOH HOH . F 6 HOH A 37 537 411 HOH HOH . F 6 HOH A 38 538 534 HOH HOH . F 6 HOH A 39 539 465 HOH HOH . F 6 HOH A 40 540 400 HOH HOH . F 6 HOH A 41 541 548 HOH HOH . F 6 HOH A 42 542 563 HOH HOH . F 6 HOH A 43 543 500 HOH HOH . F 6 HOH A 44 544 402 HOH HOH . F 6 HOH A 45 545 447 HOH HOH . F 6 HOH A 46 546 549 HOH HOH . F 6 HOH A 47 547 393 HOH HOH . F 6 HOH A 48 548 434 HOH HOH . F 6 HOH A 49 549 458 HOH HOH . F 6 HOH A 50 550 507 HOH HOH . F 6 HOH A 51 551 583 HOH HOH . F 6 HOH A 52 552 433 HOH HOH . F 6 HOH A 53 553 538 HOH HOH . F 6 HOH A 54 554 536 HOH HOH . F 6 HOH A 55 555 577 HOH HOH . F 6 HOH A 56 556 404 HOH HOH . F 6 HOH A 57 557 408 HOH HOH . F 6 HOH A 58 558 569 HOH HOH . F 6 HOH A 59 559 901 HOH HOH . F 6 HOH A 60 560 499 HOH HOH . F 6 HOH A 61 561 579 HOH HOH . F 6 HOH A 62 562 497 HOH HOH . F 6 HOH A 63 563 419 HOH HOH . F 6 HOH A 64 564 428 HOH HOH . F 6 HOH A 65 565 541 HOH HOH . F 6 HOH A 66 566 490 HOH HOH . F 6 HOH A 67 567 412 HOH HOH . F 6 HOH A 68 568 438 HOH HOH . F 6 HOH A 69 569 459 HOH HOH . F 6 HOH A 70 570 420 HOH HOH . F 6 HOH A 71 571 503 HOH HOH . F 6 HOH A 72 572 441 HOH HOH . F 6 HOH A 73 573 545 HOH HOH . F 6 HOH A 74 574 482 HOH HOH . F 6 HOH A 75 575 429 HOH HOH . F 6 HOH A 76 576 519 HOH HOH . F 6 HOH A 77 577 529 HOH HOH . F 6 HOH A 78 578 418 HOH HOH . F 6 HOH A 79 579 413 HOH HOH . F 6 HOH A 80 580 473 HOH HOH . F 6 HOH A 81 581 443 HOH HOH . F 6 HOH A 82 582 435 HOH HOH . F 6 HOH A 83 583 568 HOH HOH . F 6 HOH A 84 584 390 HOH HOH . F 6 HOH A 85 585 531 HOH HOH . F 6 HOH A 86 586 455 HOH HOH . F 6 HOH A 87 587 547 HOH HOH . F 6 HOH A 88 588 562 HOH HOH . F 6 HOH A 89 589 437 HOH HOH . F 6 HOH A 90 590 446 HOH HOH . F 6 HOH A 91 591 484 HOH HOH . F 6 HOH A 92 592 406 HOH HOH . F 6 HOH A 93 593 509 HOH HOH . F 6 HOH A 94 594 554 HOH HOH . F 6 HOH A 95 595 414 HOH HOH . F 6 HOH A 96 596 399 HOH HOH . F 6 HOH A 97 597 476 HOH HOH . F 6 HOH A 98 598 532 HOH HOH . F 6 HOH A 99 599 540 HOH HOH . F 6 HOH A 100 600 388 HOH HOH . F 6 HOH A 101 601 460 HOH HOH . F 6 HOH A 102 602 502 HOH HOH . F 6 HOH A 103 603 474 HOH HOH . F 6 HOH A 104 604 407 HOH HOH . F 6 HOH A 105 605 496 HOH HOH . F 6 HOH A 106 606 555 HOH HOH . F 6 HOH A 107 607 396 HOH HOH . F 6 HOH A 108 608 463 HOH HOH . F 6 HOH A 109 609 1001 HOH HOH . F 6 HOH A 110 610 539 HOH HOH . F 6 HOH A 111 611 567 HOH HOH . F 6 HOH A 112 612 457 HOH HOH . F 6 HOH A 113 613 571 HOH HOH . F 6 HOH A 114 614 526 HOH HOH . F 6 HOH A 115 615 492 HOH HOH . F 6 HOH A 116 616 449 HOH HOH . F 6 HOH A 117 617 530 HOH HOH . F 6 HOH A 118 618 556 HOH HOH . F 6 HOH A 119 619 477 HOH HOH . F 6 HOH A 120 620 481 HOH HOH . F 6 HOH A 121 621 423 HOH HOH . F 6 HOH A 122 622 415 HOH HOH . F 6 HOH A 123 623 471 HOH HOH . F 6 HOH A 124 624 485 HOH HOH . F 6 HOH A 125 625 527 HOH HOH . F 6 HOH A 126 626 401 HOH HOH . F 6 HOH A 127 627 421 HOH HOH . F 6 HOH A 128 628 472 HOH HOH . F 6 HOH A 129 629 566 HOH HOH . F 6 HOH A 130 630 544 HOH HOH . F 6 HOH A 131 631 1201 HOH HOH . F 6 HOH A 132 632 505 HOH HOH . F 6 HOH A 133 633 581 HOH HOH . F 6 HOH A 134 634 403 HOH HOH . F 6 HOH A 135 635 479 HOH HOH . F 6 HOH A 136 636 582 HOH HOH . F 6 HOH A 137 637 513 HOH HOH . F 6 HOH A 138 638 552 HOH HOH . F 6 HOH A 139 639 480 HOH HOH . F 6 HOH A 140 640 565 HOH HOH . F 6 HOH A 141 641 397 HOH HOH . F 6 HOH A 142 642 570 HOH HOH . F 6 HOH A 143 643 518 HOH HOH . F 6 HOH A 144 644 427 HOH HOH . F 6 HOH A 145 645 498 HOH HOH . F 6 HOH A 146 646 488 HOH HOH . F 6 HOH A 147 647 395 HOH HOH . F 6 HOH A 148 648 483 HOH HOH . F 6 HOH A 149 649 424 HOH HOH . F 6 HOH A 150 650 430 HOH HOH . F 6 HOH A 151 651 560 HOH HOH . F 6 HOH A 152 652 542 HOH HOH . F 6 HOH A 153 653 576 HOH HOH . F 6 HOH A 154 654 425 HOH HOH . F 6 HOH A 155 655 462 HOH HOH . F 6 HOH A 156 656 572 HOH HOH . F 6 HOH A 157 657 466 HOH HOH . F 6 HOH A 158 658 440 HOH HOH . F 6 HOH A 159 659 442 HOH HOH . F 6 HOH A 160 660 524 HOH HOH . F 6 HOH A 161 661 506 HOH HOH . F 6 HOH A 162 662 543 HOH HOH . F 6 HOH A 163 663 559 HOH HOH . F 6 HOH A 164 664 410 HOH HOH . F 6 HOH A 165 665 436 HOH HOH . F 6 HOH A 166 666 454 HOH HOH . F 6 HOH A 167 667 469 HOH HOH . F 6 HOH A 168 668 489 HOH HOH . F 6 HOH A 169 669 486 HOH HOH . F 6 HOH A 170 670 504 HOH HOH . F 6 HOH A 171 671 551 HOH HOH . F 6 HOH A 172 672 557 HOH HOH . F 6 HOH A 173 673 451 HOH HOH . F 6 HOH A 174 674 494 HOH HOH . F 6 HOH A 175 675 578 HOH HOH . F 6 HOH A 176 676 533 HOH HOH . F 6 HOH A 177 677 422 HOH HOH . F 6 HOH A 178 678 517 HOH HOH . F 6 HOH A 179 679 468 HOH HOH . F 6 HOH A 180 680 535 HOH HOH . F 6 HOH A 181 681 522 HOH HOH . F 6 HOH A 182 682 516 HOH HOH . F 6 HOH A 183 683 392 HOH HOH . F 6 HOH A 184 684 452 HOH HOH . F 6 HOH A 185 685 561 HOH HOH . F 6 HOH A 186 686 426 HOH HOH . F 6 HOH A 187 687 405 HOH HOH . F 6 HOH A 188 688 493 HOH HOH . F 6 HOH A 189 689 520 HOH HOH . F 6 HOH A 190 690 495 HOH HOH . F 6 HOH A 191 691 394 HOH HOH . F 6 HOH A 192 692 512 HOH HOH . F 6 HOH A 193 693 391 HOH HOH . F 6 HOH A 194 694 574 HOH HOH . F 6 HOH A 195 695 501 HOH HOH . F 6 HOH A 196 696 546 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 PB ADP . . . B 2 -11.739 33.683 4.824 1 35.25 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -11.738 34.936 4.07 1 32.66 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -10.977 32.611 4.106 1 32.12 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -11.295 33.864 6.233 1 29.46 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -14.118 32.05 4.268 1 24.32 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -13.439 31.576 3.035 1 26.91 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -14.378 31.06 5.348 1 28.54 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -13.288 33.264 4.89 1 29.91 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -15.479 32.775 3.868 1 28.37 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -16.512 32.859 4.867 1 27.19 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -17.679 33.618 4.295 1 21.02 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -18.444 32.726 3.451 1 21.08 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -18.677 34.172 5.318 1 22.56 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -19.212 35.406 4.863 1 21.58 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -19.743 33.077 5.347 1 22.46 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -21.012 33.521 5.763 1 20.85 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -19.783 32.704 3.876 1 20.71 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -20.336 31.382 3.632 1 19.35 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -19.94 30.196 4.192 1 18.84 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -20.639 29.171 3.778 1 17.28 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -21.557 29.717 2.895 1 18.66 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -22.585 29.149 2.123 1 19.74 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -22.878 27.853 2.116 1 16.19 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -23.316 29.985 1.352 1 19.44 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -23.027 31.289 1.362 1 16.22 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -22.088 31.933 2.042 1 18.43 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -21.383 31.083 2.801 1 18.67 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 30 _model_server_stats.element_count 27 #