data_8YSE # _model_server_result.job_id ZSdEzNfwmwUggzss5mhofQ _model_server_result.datetime_utc '2025-02-05 03:33:44' _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 8yse # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8YSE # _exptl.entry_id 8YSE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 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 99.56 _cell.angle_beta 105.81 _cell.angle_gamma 100.12 _cell.entry_id 8YSE _cell.length_a 35.355 _cell.length_b 46.614 _cell.length_c 59.644 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YSE _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 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 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc2 A OD2 ASP 78 A ASP 78 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 A OD2 ASP 78 A ASP 78 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc4 A OD2 ASP 80 A ASP 80 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc5 A OD1 ASP 80 A ASP 80 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc6 A OD2 ASP 129 A ASP 129 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc7 B O1A DTP . A DTP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc8 B O2G DTP . A DTP 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc9 B O1B DTP . A DTP 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc10 B O1A DTP . A DTP 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? # _chem_comp.formula 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 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 DTP doub 83 n n PG O2G DTP sing 84 n n PG O3G DTP sing 85 n n PG O3B DTP sing 86 n n O2G HOG2 DTP sing 87 n n O3G HOG3 DTP sing 88 n n PB O1B DTP doub 89 n n PB O2B DTP sing 90 n n PB O3B DTP sing 91 n n PB O3A DTP sing 92 n n O2B HOB2 DTP sing 93 n n PA O1A DTP doub 94 n n PA O2A DTP sing 95 n n PA O3A DTP sing 96 n n PA O5' DTP sing 97 n n O2A HOA2 DTP sing 98 n n O5' C5' DTP sing 99 n n C5' C4' DTP sing 100 n n C5' "H5'1" DTP sing 101 n n C5' "H5'2" DTP sing 102 n n C4' O4' DTP sing 103 n n C4' C3' DTP sing 104 n n C4' H4' DTP sing 105 n n O4' C1' DTP sing 106 n n C3' O3' DTP sing 107 n n C3' C2' DTP sing 108 n n C3' H3' DTP sing 109 n n O3' HO3' DTP sing 110 n n C2' C1' DTP sing 111 n n C2' "H2'1" DTP sing 112 n n C2' "H2'2" DTP sing 113 n n C1' N9 DTP sing 114 n n C1' H1' DTP sing 115 n n N9 C8 DTP sing 116 n y N9 C4 DTP sing 117 n y C8 N7 DTP doub 118 n y C8 H8 DTP sing 119 n n N7 C5 DTP sing 120 n y C5 C6 DTP sing 121 n y C5 C4 DTP doub 122 n y C6 N6 DTP sing 123 n n C6 N1 DTP doub 124 n y N6 HN61 DTP sing 125 n n N6 HN62 DTP sing 126 n n N1 C2 DTP sing 127 n y C2 N3 DTP doub 128 n y C2 H2 DTP sing 129 n n N3 C4 DTP sing 130 n y # _atom_sites.entry_id 8YSE _atom_sites.fract_transf_matrix[1][1] 0.028285 _atom_sites.fract_transf_matrix[1][2] 0.00505 _atom_sites.fract_transf_matrix[1][3] 0.009394 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021792 _atom_sites.fract_transf_matrix[2][3] 0.005054 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.017888 _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 DTP A 1 401 350 DTP DTP . C 2 DTP A 1 402 351 DTP DTP . D 3 MG A 1 403 360 MG MG . E 3 MG A 1 404 361 MG MG . F 4 HOH A 1 501 529 HOH HOH . F 4 HOH A 2 502 506 HOH HOH . F 4 HOH A 3 503 526 HOH HOH . F 4 HOH A 4 504 535 HOH HOH . F 4 HOH A 5 505 536 HOH HOH . F 4 HOH A 6 506 418 HOH HOH . F 4 HOH A 7 507 415 HOH HOH . F 4 HOH A 8 508 543 HOH HOH . F 4 HOH A 9 509 525 HOH HOH . F 4 HOH A 10 510 437 HOH HOH . F 4 HOH A 11 511 498 HOH HOH . F 4 HOH A 12 512 447 HOH HOH . F 4 HOH A 13 513 400 HOH HOH . F 4 HOH A 14 514 452 HOH HOH . F 4 HOH A 15 515 422 HOH HOH . F 4 HOH A 16 516 466 HOH HOH . F 4 HOH A 17 517 444 HOH HOH . F 4 HOH A 18 518 440 HOH HOH . F 4 HOH A 19 519 420 HOH HOH . F 4 HOH A 20 520 429 HOH HOH . F 4 HOH A 21 521 476 HOH HOH . F 4 HOH A 22 522 503 HOH HOH . F 4 HOH A 23 523 490 HOH HOH . F 4 HOH A 24 524 419 HOH HOH . F 4 HOH A 25 525 421 HOH HOH . F 4 HOH A 26 526 468 HOH HOH . F 4 HOH A 27 527 483 HOH HOH . F 4 HOH A 28 528 521 HOH HOH . F 4 HOH A 29 529 449 HOH HOH . F 4 HOH A 30 530 469 HOH HOH . F 4 HOH A 31 531 539 HOH HOH . F 4 HOH A 32 532 450 HOH HOH . F 4 HOH A 33 533 479 HOH HOH . F 4 HOH A 34 534 542 HOH HOH . F 4 HOH A 35 535 410 HOH HOH . F 4 HOH A 36 536 472 HOH HOH . F 4 HOH A 37 537 491 HOH HOH . F 4 HOH A 38 538 433 HOH HOH . F 4 HOH A 39 539 416 HOH HOH . F 4 HOH A 40 540 436 HOH HOH . F 4 HOH A 41 541 427 HOH HOH . F 4 HOH A 42 542 500 HOH HOH . F 4 HOH A 43 543 403 HOH HOH . F 4 HOH A 44 544 409 HOH HOH . F 4 HOH A 45 545 408 HOH HOH . F 4 HOH A 46 546 470 HOH HOH . F 4 HOH A 47 547 402 HOH HOH . F 4 HOH A 48 548 477 HOH HOH . F 4 HOH A 49 549 532 HOH HOH . F 4 HOH A 50 550 439 HOH HOH . F 4 HOH A 51 551 441 HOH HOH . F 4 HOH A 52 552 459 HOH HOH . F 4 HOH A 53 553 445 HOH HOH . F 4 HOH A 54 554 411 HOH HOH . F 4 HOH A 55 555 519 HOH HOH . F 4 HOH A 56 556 428 HOH HOH . F 4 HOH A 57 557 442 HOH HOH . F 4 HOH A 58 558 404 HOH HOH . F 4 HOH A 59 559 501 HOH HOH . F 4 HOH A 60 560 423 HOH HOH . F 4 HOH A 61 561 430 HOH HOH . F 4 HOH A 62 562 471 HOH HOH . F 4 HOH A 63 563 401 HOH HOH . F 4 HOH A 64 564 456 HOH HOH . F 4 HOH A 65 565 473 HOH HOH . F 4 HOH A 66 566 481 HOH HOH . F 4 HOH A 67 567 424 HOH HOH . F 4 HOH A 68 568 455 HOH HOH . F 4 HOH A 69 569 405 HOH HOH . F 4 HOH A 70 570 502 HOH HOH . F 4 HOH A 71 571 425 HOH HOH . F 4 HOH A 72 572 434 HOH HOH . F 4 HOH A 73 573 448 HOH HOH . F 4 HOH A 74 574 467 HOH HOH . F 4 HOH A 75 575 480 HOH HOH . F 4 HOH A 76 576 431 HOH HOH . F 4 HOH A 77 577 438 HOH HOH . F 4 HOH A 78 578 523 HOH HOH . F 4 HOH A 79 579 435 HOH HOH . F 4 HOH A 80 580 486 HOH HOH . F 4 HOH A 81 581 414 HOH HOH . F 4 HOH A 82 582 475 HOH HOH . F 4 HOH A 83 583 407 HOH HOH . F 4 HOH A 84 584 474 HOH HOH . F 4 HOH A 85 585 412 HOH HOH . F 4 HOH A 86 586 461 HOH HOH . F 4 HOH A 87 587 432 HOH HOH . F 4 HOH A 88 588 426 HOH HOH . F 4 HOH A 89 589 516 HOH HOH . F 4 HOH A 90 590 510 HOH HOH . F 4 HOH A 91 591 482 HOH HOH . F 4 HOH A 92 592 457 HOH HOH . F 4 HOH A 93 593 509 HOH HOH . F 4 HOH A 94 594 514 HOH HOH . F 4 HOH A 95 595 458 HOH HOH . F 4 HOH A 96 596 446 HOH HOH . F 4 HOH A 97 597 460 HOH HOH . F 4 HOH A 98 598 508 HOH HOH . F 4 HOH A 99 599 518 HOH HOH . F 4 HOH A 100 600 465 HOH HOH . F 4 HOH A 101 601 530 HOH HOH . F 4 HOH A 102 602 496 HOH HOH . F 4 HOH A 103 603 453 HOH HOH . F 4 HOH A 104 604 517 HOH HOH . F 4 HOH A 105 605 463 HOH HOH . F 4 HOH A 106 606 451 HOH HOH . F 4 HOH A 107 607 406 HOH HOH . F 4 HOH A 108 608 478 HOH HOH . F 4 HOH A 109 609 417 HOH HOH . F 4 HOH A 110 610 484 HOH HOH . F 4 HOH A 111 611 413 HOH HOH . F 4 HOH A 112 612 443 HOH HOH . F 4 HOH A 113 613 485 HOH HOH . F 4 HOH A 114 614 488 HOH HOH . F 4 HOH A 115 615 494 HOH HOH . F 4 HOH A 116 616 545 HOH HOH . F 4 HOH A 117 617 462 HOH HOH . F 4 HOH A 118 618 497 HOH HOH . F 4 HOH A 119 619 492 HOH HOH . F 4 HOH A 120 620 454 HOH HOH . F 4 HOH A 121 621 493 HOH HOH . F 4 HOH A 122 622 520 HOH HOH . F 4 HOH A 123 623 513 HOH HOH . F 4 HOH A 124 624 505 HOH HOH . F 4 HOH A 125 625 512 HOH HOH . F 4 HOH A 126 626 522 HOH HOH . F 4 HOH A 127 627 511 HOH HOH . F 4 HOH A 128 628 464 HOH HOH . F 4 HOH A 129 629 504 HOH HOH . F 4 HOH A 130 630 541 HOH HOH . F 4 HOH A 131 631 487 HOH HOH . F 4 HOH A 132 632 489 HOH HOH . F 4 HOH A 133 633 495 HOH HOH . F 4 HOH A 134 634 507 HOH HOH . F 4 HOH A 135 635 524 HOH HOH . F 4 HOH A 136 636 528 HOH HOH . F 4 HOH A 137 637 540 HOH HOH . F 4 HOH A 138 638 544 HOH HOH . F 4 HOH A 139 639 546 HOH HOH . F 4 HOH A 140 640 499 HOH HOH . F 4 HOH A 141 641 515 HOH HOH . F 4 HOH A 142 642 538 HOH HOH . F 4 HOH A 143 643 531 HOH HOH . F 4 HOH A 144 644 533 HOH HOH . F 4 HOH A 145 645 527 HOH HOH . F 4 HOH A 146 646 534 HOH HOH . F 4 HOH A 147 647 537 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 DTP . . . B 2 0.905 2.398 -1.18 0.77 22.11 ? PG DTP 401 A 1 HETATM 2 O O1G DTP . . . B 2 2.179 1.996 -0.563 0.77 24.05 ? O1G DTP 401 A 1 HETATM 3 O O2G DTP . . . B 2 0.923 2.581 -2.685 0.77 18.46 ? O2G DTP 401 A 1 HETATM 4 O O3G DTP . . . B 2 0.44 3.596 -0.445 0.77 24.39 ? O3G DTP 401 A 1 HETATM 5 P PB DTP . . . B 2 -1.424 0.676 -1.527 0.77 24.48 ? PB DTP 401 A 1 HETATM 6 O O1B DTP . . . B 2 -1.973 1.639 -2.557 0.77 26.27 ? O1B DTP 401 A 1 HETATM 7 O O2B DTP . . . B 2 -2.352 0.356 -0.325 0.77 25.84 ? O2B DTP 401 A 1 HETATM 8 O O3B DTP . . . B 2 -0.148 1.276 -0.763 0.77 22.34 ? O3B DTP 401 A 1 HETATM 9 P PA DTP . . . B 2 -0.142 -0.886 -3.701 0.77 23.51 ? PA DTP 401 A 1 HETATM 10 O O1A DTP . . . B 2 -0.162 0.353 -4.551 0.77 21.88 ? O1A DTP 401 A 1 HETATM 11 O O2A DTP . . . B 2 1.089 -1.787 -3.746 0.77 24.92 ? O2A DTP 401 A 1 HETATM 12 O O3A DTP . . . B 2 -0.652 -0.625 -2.145 0.77 23.67 ? O3A DTP 401 A 1 HETATM 13 O O5' DTP . . . B 2 -1.349 -1.832 -4.145 0.77 25.11 ? O5' DTP 401 A 1 HETATM 14 C C5' DTP . . . B 2 -2.574 -1.239 -4.603 0.77 27.33 ? C5' DTP 401 A 1 HETATM 15 C C4' DTP . . . B 2 -3.743 -2.153 -4.326 0.77 28.78 ? C4' DTP 401 A 1 HETATM 16 O O4' DTP . . . B 2 -3.648 -3.331 -5.139 0.77 29.17 ? O4' DTP 401 A 1 HETATM 17 C C3' DTP . . . B 2 -3.76 -2.642 -2.884 0.77 30.53 ? C3' DTP 401 A 1 HETATM 18 O O3' DTP . . . B 2 -4.396 -1.693 -2.051 0.77 29.28 ? O3' DTP 401 A 1 HETATM 19 C C2' DTP . . . B 2 -4.48 -3.99 -3.017 0.77 32.92 ? C2' DTP 401 A 1 HETATM 20 C C1' DTP . . . B 2 -3.973 -4.494 -4.377 0.77 29.98 ? C1' DTP 401 A 1 HETATM 21 N N9 DTP . . . B 2 -2.726 -5.279 -4.149 0.77 30.77 ? N9 DTP 401 A 1 HETATM 22 C C8 DTP . . . B 2 -1.457 -4.843 -4.286 0.77 29.88 ? C8 DTP 401 A 1 HETATM 23 N N7 DTP . . . B 2 -0.559 -5.822 -3.948 0.77 28.42 ? N7 DTP 401 A 1 HETATM 24 C C5 DTP . . . B 2 -1.238 -6.88 -3.547 0.77 30.58 ? C5 DTP 401 A 1 HETATM 25 C C6 DTP . . . B 2 -0.894 -8.242 -3.077 0.77 30.19 ? C6 DTP 401 A 1 HETATM 26 N N6 DTP . . . B 2 0.365 -8.647 -2.954 0.77 29.72 ? N6 DTP 401 A 1 HETATM 27 N N1 DTP . . . B 2 -1.888 -9.058 -2.797 0.77 29.29 ? N1 DTP 401 A 1 HETATM 28 C C2 DTP . . . B 2 -3.168 -8.66 -2.959 0.77 30.39 ? C2 DTP 401 A 1 HETATM 29 N N3 DTP . . . B 2 -3.549 -7.444 -3.342 0.77 28.19 ? N3 DTP 401 A 1 HETATM 30 C C4 DTP . . . B 2 -2.655 -6.531 -3.669 0.77 29.83 ? C4 DTP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 30 #