data_8YSC # _model_server_result.job_id GPdE4FEq-xqVshnJ5FrSPQ _model_server_result.datetime_utc '2025-02-12 03:34:21' _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 8ysc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8YSC # _exptl.entry_id 8YSC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 99.69 _cell.angle_beta 106.07 _cell.angle_gamma 99.37 _cell.entry_id 8YSC _cell.length_a 35.343 _cell.length_b 46.559 _cell.length_c 59.78 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YSC _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N 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 A OD1 ASP 78 A ASP 78 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc2 A OD2 ASP 78 A ASP 78 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc3 A OD2 ASP 78 A ASP 78 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc4 A OD2 ASP 80 A ASP 80 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc5 A OD1 ASP 80 A ASP 80 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc6 A OD2 ASP 129 A ASP 129 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc7 B O2A ATP . A ATP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc8 B O3G ATP . A ATP 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc9 B O1B ATP . A ATP 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc10 B O2A ATP . A ATP 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc11 C O3' ATP . A ATP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc12 C O2' ATP . A ATP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc13 D MG MG . A MG 403 1_555 F O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc14 E MG MG . A MG 404 1_555 F O HOH . A HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 8YSC _atom_sites.fract_transf_matrix[1][1] 0.028294 _atom_sites.fract_transf_matrix[1][2] 0.004667 _atom_sites.fract_transf_matrix[1][3] 0.009444 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021768 _atom_sites.fract_transf_matrix[2][3] 0.005028 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.017867 _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 ATP A 1 401 350 ATP ATP . C 2 ATP A 1 402 351 ATP ATP . D 3 MG A 1 403 360 MG MG . E 3 MG A 1 404 361 MG MG . F 4 HOH A 1 501 507 HOH HOH . F 4 HOH A 2 502 513 HOH HOH . F 4 HOH A 3 503 490 HOH HOH . F 4 HOH A 4 504 515 HOH HOH . F 4 HOH A 5 505 440 HOH HOH . F 4 HOH A 6 506 429 HOH HOH . F 4 HOH A 7 507 422 HOH HOH . F 4 HOH A 8 508 465 HOH HOH . F 4 HOH A 9 509 437 HOH HOH . F 4 HOH A 10 510 509 HOH HOH . F 4 HOH A 11 511 406 HOH HOH . F 4 HOH A 12 512 456 HOH HOH . F 4 HOH A 13 513 416 HOH HOH . F 4 HOH A 14 514 466 HOH HOH . F 4 HOH A 15 515 459 HOH HOH . F 4 HOH A 16 516 463 HOH HOH . F 4 HOH A 17 517 436 HOH HOH . F 4 HOH A 18 518 462 HOH HOH . F 4 HOH A 19 519 508 HOH HOH . F 4 HOH A 20 520 403 HOH HOH . F 4 HOH A 21 521 486 HOH HOH . F 4 HOH A 22 522 401 HOH HOH . F 4 HOH A 23 523 474 HOH HOH . F 4 HOH A 24 524 431 HOH HOH . F 4 HOH A 25 525 498 HOH HOH . F 4 HOH A 26 526 413 HOH HOH . F 4 HOH A 27 527 473 HOH HOH . F 4 HOH A 28 528 423 HOH HOH . F 4 HOH A 29 529 458 HOH HOH . F 4 HOH A 30 530 438 HOH HOH . F 4 HOH A 31 531 455 HOH HOH . F 4 HOH A 32 532 450 HOH HOH . F 4 HOH A 33 533 445 HOH HOH . F 4 HOH A 34 534 460 HOH HOH . F 4 HOH A 35 535 468 HOH HOH . F 4 HOH A 36 536 400 HOH HOH . F 4 HOH A 37 537 441 HOH HOH . F 4 HOH A 38 538 442 HOH HOH . F 4 HOH A 39 539 411 HOH HOH . F 4 HOH A 40 540 448 HOH HOH . F 4 HOH A 41 541 410 HOH HOH . F 4 HOH A 42 542 504 HOH HOH . F 4 HOH A 43 543 500 HOH HOH . F 4 HOH A 44 544 434 HOH HOH . F 4 HOH A 45 545 409 HOH HOH . F 4 HOH A 46 546 452 HOH HOH . F 4 HOH A 47 547 481 HOH HOH . F 4 HOH A 48 548 457 HOH HOH . F 4 HOH A 49 549 421 HOH HOH . F 4 HOH A 50 550 407 HOH HOH . F 4 HOH A 51 551 404 HOH HOH . F 4 HOH A 52 552 447 HOH HOH . F 4 HOH A 53 553 405 HOH HOH . F 4 HOH A 54 554 430 HOH HOH . F 4 HOH A 55 555 464 HOH HOH . F 4 HOH A 56 556 469 HOH HOH . F 4 HOH A 57 557 414 HOH HOH . F 4 HOH A 58 558 420 HOH HOH . F 4 HOH A 59 559 425 HOH HOH . F 4 HOH A 60 560 511 HOH HOH . F 4 HOH A 61 561 480 HOH HOH . F 4 HOH A 62 562 503 HOH HOH . F 4 HOH A 63 563 432 HOH HOH . F 4 HOH A 64 564 435 HOH HOH . F 4 HOH A 65 565 451 HOH HOH . F 4 HOH A 66 566 428 HOH HOH . F 4 HOH A 67 567 418 HOH HOH . F 4 HOH A 68 568 402 HOH HOH . F 4 HOH A 69 569 488 HOH HOH . F 4 HOH A 70 570 487 HOH HOH . F 4 HOH A 71 571 510 HOH HOH . F 4 HOH A 72 572 433 HOH HOH . F 4 HOH A 73 573 417 HOH HOH . F 4 HOH A 74 574 492 HOH HOH . F 4 HOH A 75 575 470 HOH HOH . F 4 HOH A 76 576 485 HOH HOH . F 4 HOH A 77 577 419 HOH HOH . F 4 HOH A 78 578 482 HOH HOH . F 4 HOH A 79 579 408 HOH HOH . F 4 HOH A 80 580 499 HOH HOH . F 4 HOH A 81 581 454 HOH HOH . F 4 HOH A 82 582 479 HOH HOH . F 4 HOH A 83 583 478 HOH HOH . F 4 HOH A 84 584 443 HOH HOH . F 4 HOH A 85 585 496 HOH HOH . F 4 HOH A 86 586 453 HOH HOH . F 4 HOH A 87 587 489 HOH HOH . F 4 HOH A 88 588 506 HOH HOH . F 4 HOH A 89 589 471 HOH HOH . F 4 HOH A 90 590 449 HOH HOH . F 4 HOH A 91 591 427 HOH HOH . F 4 HOH A 92 592 483 HOH HOH . F 4 HOH A 93 593 467 HOH HOH . F 4 HOH A 94 594 517 HOH HOH . F 4 HOH A 95 595 477 HOH HOH . F 4 HOH A 96 596 502 HOH HOH . F 4 HOH A 97 597 446 HOH HOH . F 4 HOH A 98 598 476 HOH HOH . F 4 HOH A 99 599 475 HOH HOH . F 4 HOH A 100 600 426 HOH HOH . F 4 HOH A 101 601 412 HOH HOH . F 4 HOH A 102 602 501 HOH HOH . F 4 HOH A 103 603 493 HOH HOH . F 4 HOH A 104 604 495 HOH HOH . F 4 HOH A 105 605 424 HOH HOH . F 4 HOH A 106 606 505 HOH HOH . F 4 HOH A 107 607 512 HOH HOH . F 4 HOH A 108 608 444 HOH HOH . F 4 HOH A 109 609 494 HOH HOH . F 4 HOH A 110 610 439 HOH HOH . F 4 HOH A 111 611 516 HOH HOH . F 4 HOH A 112 612 491 HOH HOH . F 4 HOH A 113 613 484 HOH HOH . F 4 HOH A 114 614 497 HOH HOH . F 4 HOH A 115 615 415 HOH HOH . F 4 HOH A 116 616 472 HOH HOH . F 4 HOH A 117 617 514 HOH HOH . F 4 HOH A 118 618 461 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 PG ATP . . . B 2 0.929 2.427 -1.219 1 22.35 ? PG ATP 401 A 1 HETATM 2 O O1G ATP . . . B 2 0.432 3.588 -0.437 1 26.52 ? O1G ATP 401 A 1 HETATM 3 O O2G ATP . . . B 2 2.196 1.844 -0.682 1 30.1 ? O2G ATP 401 A 1 HETATM 4 O O3G ATP . . . B 2 0.862 2.544 -2.692 1 24.11 ? O3G ATP 401 A 1 HETATM 5 P PB ATP . . . B 2 -1.423 0.736 -1.639 1 23.96 ? PB ATP 401 A 1 HETATM 6 O O1B ATP . . . B 2 -1.962 1.764 -2.595 1 27.31 ? O1B ATP 401 A 1 HETATM 7 O O2B ATP . . . B 2 -2.454 0.275 -0.679 1 25.61 ? O2B ATP 401 A 1 HETATM 8 O O3B ATP . . . B 2 -0.214 1.348 -0.774 1 24.37 ? O3B ATP 401 A 1 HETATM 9 P PA ATP . . . B 2 -0.192 -0.814 -3.795 1 21.69 ? PA ATP 401 A 1 HETATM 10 O O1A ATP . . . B 2 1.01 -1.736 -3.788 1 21.83 ? O1A ATP 401 A 1 HETATM 11 O O2A ATP . . . B 2 -0.159 0.483 -4.522 1 20.12 ? O2A ATP 401 A 1 HETATM 12 O O3A ATP . . . B 2 -0.703 -0.587 -2.271 1 22.11 ? O3A ATP 401 A 1 HETATM 13 O O5' ATP . . . B 2 -1.399 -1.724 -4.33 1 23.04 ? O5' ATP 401 A 1 HETATM 14 C C5' ATP . . . B 2 -2.619 -1.12 -4.667 1 25.63 ? C5' ATP 401 A 1 HETATM 15 C C4' ATP . . . B 2 -3.763 -2.018 -4.248 1 26.04 ? C4' ATP 401 A 1 HETATM 16 O O4' ATP . . . B 2 -3.664 -3.246 -5.005 1 27.85 ? O4' ATP 401 A 1 HETATM 17 C C3' ATP . . . B 2 -3.795 -2.385 -2.775 1 27.35 ? C3' ATP 401 A 1 HETATM 18 O O3' ATP . . . B 2 -4.323 -1.34 -1.917 1 28.19 ? O3' ATP 401 A 1 HETATM 19 C C2' ATP . . . B 2 -4.575 -3.7 -2.864 1 31.02 ? C2' ATP 401 A 1 HETATM 20 O O2' ATP . . . B 2 -5.995 -3.545 -2.996 1 27.46 ? O2' ATP 401 A 1 HETATM 21 C C1' ATP . . . B 2 -4.037 -4.344 -4.183 1 27.44 ? C1' ATP 401 A 1 HETATM 22 N N9 ATP . . . B 2 -2.829 -5.158 -3.939 1 28.14 ? N9 ATP 401 A 1 HETATM 23 C C8 ATP . . . B 2 -1.545 -4.727 -4.048 1 27.41 ? C8 ATP 401 A 1 HETATM 24 N N7 ATP . . . B 2 -0.669 -5.713 -3.719 1 26.92 ? N7 ATP 401 A 1 HETATM 25 C C5 ATP . . . B 2 -1.38 -6.787 -3.402 1 27.83 ? C5 ATP 401 A 1 HETATM 26 C C6 ATP . . . B 2 -1.052 -8.169 -2.997 1 28.48 ? C6 ATP 401 A 1 HETATM 27 N N6 ATP . . . B 2 0.214 -8.521 -2.883 1 28.29 ? N6 ATP 401 A 1 HETATM 28 N N1 ATP . . . B 2 -2.05 -9.028 -2.729 1 27 ? N1 ATP 401 A 1 HETATM 29 C C2 ATP . . . B 2 -3.332 -8.608 -2.911 1 26.74 ? C2 ATP 401 A 1 HETATM 30 N N3 ATP . . . B 2 -3.694 -7.362 -3.279 1 25.19 ? N3 ATP 401 A 1 HETATM 31 C C4 ATP . . . B 2 -2.793 -6.43 -3.519 1 26.79 ? C4 ATP 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 31 #