data_8T8U # _model_server_result.job_id ZYSg-eBiw1gOANWGCW0G5Q _model_server_result.datetime_utc '2024-11-27 20:11:35' _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 8t8u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8T8U # _exptl.entry_id 8T8U _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 90 _cell.entry_id 8T8U _cell.length_a 61.929 _cell.length_b 104.902 _cell.length_c 102.395 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8T8U _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 # _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 A OD2 ASP 231 A ASP 231 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc2 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc3 B O1A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc4 C MG MG . A MG 402 1_555 E O1 PO4 . A PO4 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc5 C MG MG . A MG 402 1_555 F O HOH . A HOH 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc6 C MG MG . A MG 402 1_555 F O HOH . A HOH 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc7 D MG MG . A MG 403 1_555 F O HOH . A HOH 532 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc8 D MG MG . A MG 403 1_555 F O HOH . A HOH 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc9 D MG MG . A MG 403 1_555 F O HOH . A HOH 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc10 D MG MG . A MG 403 1_555 F O HOH . A HOH 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc11 D MG MG . A MG 403 1_555 F O HOH . A HOH 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc12 D MG MG . A MG 403 1_555 F O HOH . A HOH 667 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? # _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 8T8U _atom_sites.fract_transf_matrix[1][1] 0.016148 _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] 0.009533 _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] 0.009766 _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 1 401 401 ADP ADP . C 3 MG A 1 402 501 MG MG . D 3 MG A 1 403 503 MG MG . E 4 PO4 A 1 404 701 PO4 PO4 . F 5 HOH A 1 501 109 HOH HOH . F 5 HOH A 2 502 140 HOH HOH . F 5 HOH A 3 503 121 HOH HOH . F 5 HOH A 4 504 95 HOH HOH . F 5 HOH A 5 505 96 HOH HOH . F 5 HOH A 6 506 55 HOH HOH . F 5 HOH A 7 507 111 HOH HOH . F 5 HOH A 8 508 132 HOH HOH . F 5 HOH A 9 509 42 HOH HOH . F 5 HOH A 10 510 61 HOH HOH . F 5 HOH A 11 511 16 HOH HOH . F 5 HOH A 12 512 85 HOH HOH . F 5 HOH A 13 513 137 HOH HOH . F 5 HOH A 14 514 155 HOH HOH . F 5 HOH A 15 515 14 HOH HOH . F 5 HOH A 16 516 69 HOH HOH . F 5 HOH A 17 517 26 HOH HOH . F 5 HOH A 18 518 131 HOH HOH . F 5 HOH A 19 519 24 HOH HOH . F 5 HOH A 20 520 104 HOH HOH . F 5 HOH A 21 521 31 HOH HOH . F 5 HOH A 22 522 141 HOH HOH . F 5 HOH A 23 523 30 HOH HOH . F 5 HOH A 24 524 43 HOH HOH . F 5 HOH A 25 525 37 HOH HOH . F 5 HOH A 26 526 4 HOH HOH . F 5 HOH A 27 527 84 HOH HOH . F 5 HOH A 28 528 15 HOH HOH . F 5 HOH A 29 529 125 HOH HOH . F 5 HOH A 30 530 151 HOH HOH . F 5 HOH A 31 531 2 HOH HOH . F 5 HOH A 32 532 115 HOH HOH . F 5 HOH A 33 533 17 HOH HOH . F 5 HOH A 34 534 53 HOH HOH . F 5 HOH A 35 535 133 HOH HOH . F 5 HOH A 36 536 101 HOH HOH . F 5 HOH A 37 537 8 HOH HOH . F 5 HOH A 38 538 48 HOH HOH . F 5 HOH A 39 539 146 HOH HOH . F 5 HOH A 40 540 158 HOH HOH . F 5 HOH A 41 541 35 HOH HOH . F 5 HOH A 42 542 34 HOH HOH . F 5 HOH A 43 543 28 HOH HOH . F 5 HOH A 44 544 156 HOH HOH . F 5 HOH A 45 545 134 HOH HOH . F 5 HOH A 46 546 70 HOH HOH . F 5 HOH A 47 547 87 HOH HOH . F 5 HOH A 48 548 91 HOH HOH . F 5 HOH A 49 549 20 HOH HOH . F 5 HOH A 50 550 119 HOH HOH . F 5 HOH A 51 551 25 HOH HOH . F 5 HOH A 52 552 112 HOH HOH . F 5 HOH A 53 553 102 HOH HOH . F 5 HOH A 54 554 149 HOH HOH . F 5 HOH A 55 555 93 HOH HOH . F 5 HOH A 56 556 105 HOH HOH . F 5 HOH A 57 557 46 HOH HOH . F 5 HOH A 58 558 33 HOH HOH . F 5 HOH A 59 559 79 HOH HOH . F 5 HOH A 60 560 39 HOH HOH . F 5 HOH A 61 561 139 HOH HOH . F 5 HOH A 62 562 76 HOH HOH . F 5 HOH A 63 563 83 HOH HOH . F 5 HOH A 64 564 23 HOH HOH . F 5 HOH A 65 565 98 HOH HOH . F 5 HOH A 66 566 12 HOH HOH . F 5 HOH A 67 567 130 HOH HOH . F 5 HOH A 68 568 11 HOH HOH . F 5 HOH A 69 569 89 HOH HOH . F 5 HOH A 70 570 150 HOH HOH . F 5 HOH A 71 571 90 HOH HOH . F 5 HOH A 72 572 118 HOH HOH . F 5 HOH A 73 573 94 HOH HOH . F 5 HOH A 74 574 81 HOH HOH . F 5 HOH A 75 575 113 HOH HOH . F 5 HOH A 76 576 58 HOH HOH . F 5 HOH A 77 577 74 HOH HOH . F 5 HOH A 78 578 114 HOH HOH . F 5 HOH A 79 579 129 HOH HOH . F 5 HOH A 80 580 5 HOH HOH . F 5 HOH A 81 581 21 HOH HOH . F 5 HOH A 82 582 41 HOH HOH . F 5 HOH A 83 583 157 HOH HOH . F 5 HOH A 84 584 19 HOH HOH . F 5 HOH A 85 585 18 HOH HOH . F 5 HOH A 86 586 51 HOH HOH . F 5 HOH A 87 587 143 HOH HOH . F 5 HOH A 88 588 13 HOH HOH . F 5 HOH A 89 589 54 HOH HOH . F 5 HOH A 90 590 1 HOH HOH . F 5 HOH A 91 591 50 HOH HOH . F 5 HOH A 92 592 88 HOH HOH . F 5 HOH A 93 593 6 HOH HOH . F 5 HOH A 94 594 9 HOH HOH . F 5 HOH A 95 595 116 HOH HOH . F 5 HOH A 96 596 92 HOH HOH . F 5 HOH A 97 597 144 HOH HOH . F 5 HOH A 98 598 108 HOH HOH . F 5 HOH A 99 599 27 HOH HOH . F 5 HOH A 100 600 80 HOH HOH . F 5 HOH A 101 601 3 HOH HOH . F 5 HOH A 102 602 152 HOH HOH . F 5 HOH A 103 603 56 HOH HOH . F 5 HOH A 104 604 75 HOH HOH . F 5 HOH A 105 605 64 HOH HOH . F 5 HOH A 106 606 38 HOH HOH . F 5 HOH A 107 607 7 HOH HOH . F 5 HOH A 108 608 22 HOH HOH . F 5 HOH A 109 609 47 HOH HOH . F 5 HOH A 110 610 68 HOH HOH . F 5 HOH A 111 611 77 HOH HOH . F 5 HOH A 112 612 52 HOH HOH . F 5 HOH A 113 613 106 HOH HOH . F 5 HOH A 114 614 154 HOH HOH . F 5 HOH A 115 615 59 HOH HOH . F 5 HOH A 116 616 65 HOH HOH . F 5 HOH A 117 617 117 HOH HOH . F 5 HOH A 118 618 44 HOH HOH . F 5 HOH A 119 619 78 HOH HOH . F 5 HOH A 120 620 62 HOH HOH . F 5 HOH A 121 621 40 HOH HOH . F 5 HOH A 122 622 29 HOH HOH . F 5 HOH A 123 623 57 HOH HOH . F 5 HOH A 124 624 126 HOH HOH . F 5 HOH A 125 625 120 HOH HOH . F 5 HOH A 126 626 165 HOH HOH . F 5 HOH A 127 627 147 HOH HOH . F 5 HOH A 128 628 32 HOH HOH . F 5 HOH A 129 629 49 HOH HOH . F 5 HOH A 130 630 10 HOH HOH . F 5 HOH A 131 631 145 HOH HOH . F 5 HOH A 132 632 163 HOH HOH . F 5 HOH A 133 633 161 HOH HOH . F 5 HOH A 134 634 160 HOH HOH . F 5 HOH A 135 635 60 HOH HOH . F 5 HOH A 136 636 110 HOH HOH . F 5 HOH A 137 637 72 HOH HOH . F 5 HOH A 138 638 122 HOH HOH . F 5 HOH A 139 639 167 HOH HOH . F 5 HOH A 140 640 128 HOH HOH . F 5 HOH A 141 641 67 HOH HOH . F 5 HOH A 142 642 123 HOH HOH . F 5 HOH A 143 643 142 HOH HOH . F 5 HOH A 144 644 153 HOH HOH . F 5 HOH A 145 645 100 HOH HOH . F 5 HOH A 146 646 162 HOH HOH . F 5 HOH A 147 647 164 HOH HOH . F 5 HOH A 148 648 36 HOH HOH . F 5 HOH A 149 649 127 HOH HOH . F 5 HOH A 150 650 166 HOH HOH . F 5 HOH A 151 651 86 HOH HOH . F 5 HOH A 152 652 148 HOH HOH . F 5 HOH A 153 653 66 HOH HOH . F 5 HOH A 154 654 71 HOH HOH . F 5 HOH A 155 655 107 HOH HOH . F 5 HOH A 156 656 138 HOH HOH . F 5 HOH A 157 657 136 HOH HOH . F 5 HOH A 158 658 99 HOH HOH . F 5 HOH A 159 659 124 HOH HOH . F 5 HOH A 160 660 168 HOH HOH . F 5 HOH A 161 661 159 HOH HOH . F 5 HOH A 162 662 45 HOH HOH . F 5 HOH A 163 663 82 HOH HOH . F 5 HOH A 164 664 63 HOH HOH . F 5 HOH A 165 665 97 HOH HOH . F 5 HOH A 166 666 103 HOH HOH . F 5 HOH A 167 667 135 HOH HOH . F 5 HOH A 168 668 73 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 -19.042 -19.256 -0.881 1 27.23 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -19.102 -20.471 -1.781 1 26.85 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -19.701 -19.489 0.449 1 26.36 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -17.652 -18.693 -0.756 1 28.05 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -20.706 -17.896 -2.971 1 24.34 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -20.521 -19.12 -3.803 1 23.74 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -20.324 -16.561 -3.527 1 25.33 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -19.912 -18.073 -1.582 1 25.46 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -22.226 -17.829 -2.463 1 24.82 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -22.709 -18.889 -1.601 1 24.36 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -24.215 -18.841 -1.554 1 24.32 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -24.632 -17.511 -1.151 1 24.56 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -24.937 -19.111 -2.878 1 24.57 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -25.224 -20.498 -3.032 1 24.33 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -26.22 -18.293 -2.719 1 23.86 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -27.196 -19.028 -2.009 1 23.16 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -25.746 -17.09 -1.904 1 23.86 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -25.36 -15.907 -2.671 1 23.59 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -24.095 -15.511 -3.039 1 23.66 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -24.067 -14.363 -3.674 1 23.36 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -25.394 -13.961 -3.708 1 22.72 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -26.024 -12.815 -4.234 1 22.58 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -25.367 -11.817 -4.822 1 21.32 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -27.367 -12.713 -4.074 1 21.75 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -28.018 -13.711 -3.463 1 22.76 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -27.534 -14.836 -2.938 1 22.73 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -26.2 -14.9 -3.087 1 22.92 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #