data_9ICA # _model_server_result.job_id coLIHAhQLUgJBcqIibWpJQ _model_server_result.datetime_utc '2024-10-26 12:28:46' _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 9ica # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":338}' # _entry.id 9ICA # _exptl.entry_id 9ICA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.247 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE)" _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 90 _cell.entry_id 9ICA _cell.length_a 178.479 _cell.length_b 57.751 _cell.length_c 48.511 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9ICA _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 5 _struct_asym.id F _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 O3' DG 7 P DG 7 1_555 E MN MN . A MN 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc2 C OD1 ASP 190 A ASP 190 1_555 D MN MN . A MN 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc3 F S1A STP . A STP 338 1_555 D MN MN . A MN 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc4 F O1G STP . A STP 338 1_555 D MN MN . A MN 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? hydrog 'DC-DG PAIR' hydrog1 A O2 DC 1 T DC 1 1_555 B N1 DG 7 P DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N1 DA 2 T DA 2 1_555 B N3 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N6 DA 2 T DA 2 1_555 B O4 DT 6 P DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DT 3 T DT 3 1_555 B N1 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 DT 3 T DT 3 1_555 B N6 DA 5 P DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 DT 4 T DT 4 1_555 B N1 DA 4 P DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O4 DT 4 T DT 4 1_555 B N6 DA 4 P DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DA 5 T DA 5 1_555 B N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N6 DA 5 T DA 5 1_555 B O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 6 T DG 6 1_555 B N3 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 6 T DG 6 1_555 B O2 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 6 T DG 6 1_555 B N4 DC 2 P DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 7 T DA 7 1_555 B N3 DT 1 P DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 7 T DA 7 1_555 B O4 DT 1 P DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O11 P3 S' _chem_comp.formula_weight 507.247 _chem_comp.id STP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 9ICA _atom_sites.fract_transf_matrix[1][1] 0.005603 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017316 _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] 0.020614 _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 D 4 MN A 1 339 339 MN MN . E 4 MN A 1 340 340 MN MN . F 5 STP A 1 338 338 STP STP . G 6 HOH T 1 512 512 HOH HOH . G 6 HOH T 2 517 517 HOH HOH . G 6 HOH T 3 525 525 HOH HOH . G 6 HOH T 4 526 526 HOH HOH . G 6 HOH T 5 535 535 HOH HOH . G 6 HOH T 6 537 537 HOH HOH . G 6 HOH T 7 545 545 HOH HOH . G 6 HOH T 8 546 546 HOH HOH . G 6 HOH T 9 547 547 HOH HOH . G 6 HOH T 10 564 564 HOH HOH . G 6 HOH T 11 585 585 HOH HOH . G 6 HOH T 12 595 595 HOH HOH . G 6 HOH T 13 597 597 HOH HOH . G 6 HOH T 14 617 617 HOH HOH . G 6 HOH T 15 634 634 HOH HOH . G 6 HOH T 16 651 651 HOH HOH . G 6 HOH T 17 652 652 HOH HOH . H 6 HOH P 1 510 510 HOH HOH . H 6 HOH P 2 511 511 HOH HOH . H 6 HOH P 3 534 534 HOH HOH . H 6 HOH P 4 566 566 HOH HOH . H 6 HOH P 5 567 567 HOH HOH . H 6 HOH P 6 568 568 HOH HOH . H 6 HOH P 7 569 569 HOH HOH . H 6 HOH P 8 570 570 HOH HOH . H 6 HOH P 9 594 594 HOH HOH . H 6 HOH P 10 599 599 HOH HOH . H 6 HOH P 11 614 614 HOH HOH . H 6 HOH P 12 615 615 HOH HOH . H 6 HOH P 13 635 635 HOH HOH . H 6 HOH P 14 648 648 HOH HOH . H 6 HOH P 15 653 653 HOH HOH . I 6 HOH A 1 501 501 HOH HOH . I 6 HOH A 2 502 502 HOH HOH . I 6 HOH A 3 503 503 HOH HOH . I 6 HOH A 4 505 505 HOH HOH . I 6 HOH A 5 506 506 HOH HOH . I 6 HOH A 6 507 507 HOH HOH . I 6 HOH A 7 508 508 HOH HOH . I 6 HOH A 8 509 509 HOH HOH . I 6 HOH A 9 513 513 HOH HOH . I 6 HOH A 10 514 514 HOH HOH . I 6 HOH A 11 515 515 HOH HOH . I 6 HOH A 12 516 516 HOH HOH . I 6 HOH A 13 518 518 HOH HOH . I 6 HOH A 14 519 519 HOH HOH . I 6 HOH A 15 520 520 HOH HOH . I 6 HOH A 16 521 521 HOH HOH . I 6 HOH A 17 522 522 HOH HOH . I 6 HOH A 18 523 523 HOH HOH . I 6 HOH A 19 524 524 HOH HOH . I 6 HOH A 20 527 527 HOH HOH . I 6 HOH A 21 528 528 HOH HOH . I 6 HOH A 22 529 529 HOH HOH . I 6 HOH A 23 530 530 HOH HOH . I 6 HOH A 24 531 531 HOH HOH . I 6 HOH A 25 533 533 HOH HOH . I 6 HOH A 26 536 536 HOH HOH . I 6 HOH A 27 538 538 HOH HOH . I 6 HOH A 28 539 539 HOH HOH . I 6 HOH A 29 541 541 HOH HOH . I 6 HOH A 30 542 542 HOH HOH . I 6 HOH A 31 543 543 HOH HOH . I 6 HOH A 32 544 544 HOH HOH . I 6 HOH A 33 550 550 HOH HOH . I 6 HOH A 34 551 551 HOH HOH . I 6 HOH A 35 552 552 HOH HOH . I 6 HOH A 36 553 553 HOH HOH . I 6 HOH A 37 555 555 HOH HOH . I 6 HOH A 38 556 556 HOH HOH . I 6 HOH A 39 557 557 HOH HOH . I 6 HOH A 40 558 558 HOH HOH . I 6 HOH A 41 560 560 HOH HOH . I 6 HOH A 42 561 561 HOH HOH . I 6 HOH A 43 562 562 HOH HOH . I 6 HOH A 44 563 563 HOH HOH . I 6 HOH A 45 565 565 HOH HOH . I 6 HOH A 46 571 571 HOH HOH . I 6 HOH A 47 575 575 HOH HOH . I 6 HOH A 48 576 576 HOH HOH . I 6 HOH A 49 577 577 HOH HOH . I 6 HOH A 50 578 578 HOH HOH . I 6 HOH A 51 579 579 HOH HOH . I 6 HOH A 52 580 580 HOH HOH . I 6 HOH A 53 581 581 HOH HOH . I 6 HOH A 54 582 582 HOH HOH . I 6 HOH A 55 583 583 HOH HOH . I 6 HOH A 56 584 584 HOH HOH . I 6 HOH A 57 589 589 HOH HOH . I 6 HOH A 58 590 590 HOH HOH . I 6 HOH A 59 591 591 HOH HOH . I 6 HOH A 60 592 592 HOH HOH . I 6 HOH A 61 593 593 HOH HOH . I 6 HOH A 62 596 596 HOH HOH . I 6 HOH A 63 600 600 HOH HOH . I 6 HOH A 64 601 601 HOH HOH . I 6 HOH A 65 602 602 HOH HOH . I 6 HOH A 66 603 603 HOH HOH . I 6 HOH A 67 604 604 HOH HOH . I 6 HOH A 68 606 606 HOH HOH . I 6 HOH A 69 607 607 HOH HOH . I 6 HOH A 70 608 608 HOH HOH . I 6 HOH A 71 610 610 HOH HOH . I 6 HOH A 72 611 611 HOH HOH . I 6 HOH A 73 612 612 HOH HOH . I 6 HOH A 74 613 613 HOH HOH . I 6 HOH A 75 616 616 HOH HOH . I 6 HOH A 76 618 618 HOH HOH . I 6 HOH A 77 620 620 HOH HOH . I 6 HOH A 78 621 621 HOH HOH . I 6 HOH A 79 622 622 HOH HOH . I 6 HOH A 80 623 623 HOH HOH . I 6 HOH A 81 624 624 HOH HOH . I 6 HOH A 82 625 625 HOH HOH . I 6 HOH A 83 626 626 HOH HOH . I 6 HOH A 84 627 627 HOH HOH . I 6 HOH A 85 628 628 HOH HOH . I 6 HOH A 86 629 629 HOH HOH . I 6 HOH A 87 631 631 HOH HOH . I 6 HOH A 88 636 636 HOH HOH . I 6 HOH A 89 637 637 HOH HOH . I 6 HOH A 90 638 638 HOH HOH . I 6 HOH A 91 639 639 HOH HOH . I 6 HOH A 92 640 640 HOH HOH . I 6 HOH A 93 641 641 HOH HOH . I 6 HOH A 94 642 642 HOH HOH . I 6 HOH A 95 643 643 HOH HOH . I 6 HOH A 96 644 644 HOH HOH . I 6 HOH A 97 645 645 HOH HOH . I 6 HOH A 98 646 646 HOH HOH . I 6 HOH A 99 647 647 HOH HOH . I 6 HOH A 100 649 649 HOH HOH . I 6 HOH A 101 650 650 HOH HOH . I 6 HOH A 102 654 654 HOH HOH . I 6 HOH A 103 655 655 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 STP . . . F 5 74.011 35.887 53.5 0.5 62.59 ? PG STP 338 A 1 HETATM 2 O O1G STP . . . F 5 74.86 35.247 52.473 0.5 59.01 ? O1G STP 338 A 1 HETATM 3 O O2G STP . . . F 5 74.674 36.524 54.672 0.5 63.53 ? O2G STP 338 A 1 HETATM 4 O O3G STP . . . F 5 72.916 34.844 53.994 0.5 62.83 ? O3G STP 338 A 1 HETATM 5 P PB STP . . . F 5 72.897 37.222 51.225 0.5 74.92 ? PB STP 338 A 1 HETATM 6 O O1B STP . . . F 5 72.876 38.695 51.096 0.5 74.87 ? O1B STP 338 A 1 HETATM 7 O O2B STP . . . F 5 73.962 36.468 50.509 0.5 75.15 ? O2B STP 338 A 1 HETATM 8 O O3B STP . . . F 5 73.044 36.928 52.756 0.5 68.09 ? O3B STP 338 A 1 HETATM 9 P PA STP . . . F 5 70.635 35.33 50.295 0.5 80.37 ? PA STP 338 A 1 HETATM 10 S S1A STP . . . F 5 71.288 34.096 50.802 0.5 79.22 ? S1A STP 338 A 1 HETATM 11 O O2A STP . . . F 5 69.166 35.445 50.529 0.5 82.89 ? O2A STP 338 A 1 HETATM 12 O O3A STP . . . F 5 71.367 36.638 50.915 0.5 80.14 ? O3A STP 338 A 1 HETATM 13 O O5' STP . . . F 5 70.93 35.496 48.73 0.5 81.15 ? O5' STP 338 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 13 #