data_6QF4 # _model_server_result.job_id w3XM57EXq9t9z2BtRJutiA _model_server_result.datetime_utc '2024-11-14 06:52:36' _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 6qf4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 6QF4 # _exptl.entry_id 6QF4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 6QF4 _cell.length_a 85.479 _cell.length_b 85.479 _cell.length_c 118.073 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QF4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 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,G _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 6 _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 A OD1 ASN 161 A ASN 163 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc2 A OD2 ASP 177 A ASP 179 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc3 B MG MG . A MG 401 1_555 F O3B ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc4 B MG MG . A MG 401 1_555 F O1A ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc5 B MG MG . A MG 401 1_555 G O HOH . A HOH 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc6 B MG MG . A MG 401 1_555 G O HOH . A HOH 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? # _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 7 n n PB O2B ADP sing 8 n n PB O3B ADP sing 9 n n PB O3A ADP sing 10 n n O2B HOB2 ADP sing 11 n n O3B HOB3 ADP sing 12 n n PA O1A ADP doub 13 n n PA O2A ADP sing 14 n n PA O3A ADP sing 15 n n PA O5' ADP sing 16 n n O2A HOA2 ADP sing 17 n n O5' C5' ADP sing 18 n n C5' C4' ADP sing 19 n n C5' "H5'1" ADP sing 20 n n C5' "H5'2" ADP sing 21 n n C4' O4' ADP sing 22 n n C4' C3' ADP sing 23 n n C4' H4' ADP sing 24 n n O4' C1' ADP sing 25 n n C3' O3' ADP sing 26 n n C3' C2' ADP sing 27 n n C3' H3' ADP sing 28 n n O3' HO3' ADP sing 29 n n C2' O2' ADP sing 30 n n C2' C1' ADP sing 31 n n C2' H2' ADP sing 32 n n O2' HO2' ADP sing 33 n n C1' N9 ADP sing 34 n n C1' H1' ADP sing 35 n n N9 C8 ADP sing 36 n y N9 C4 ADP sing 37 n y C8 N7 ADP doub 38 n y C8 H8 ADP sing 39 n n N7 C5 ADP sing 40 n y C5 C6 ADP sing 41 n y C5 C4 ADP doub 42 n y C6 N6 ADP sing 43 n n C6 N1 ADP doub 44 n y N6 HN61 ADP sing 45 n n N6 HN62 ADP sing 46 n n N1 C2 ADP sing 47 n y C2 N3 ADP doub 48 n y C2 H2 ADP sing 49 n n N3 C4 ADP sing 50 n y # _atom_sites.entry_id 6QF4 _atom_sites.fract_transf_matrix[1][1] 0.011699 _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] 0.011699 _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] 0.008469 _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 MG A 1 401 1 MG MG . C 3 CL A 1 402 1 CL CL . D 4 EDO A 1 403 1 EDO EDO . E 5 ACT A 1 404 1 ACT ACT . F 6 ADP A 1 405 1 ADP ADP . G 7 HOH A 1 501 64 HOH HOH . G 7 HOH A 2 502 24 HOH HOH . G 7 HOH A 3 503 93 HOH HOH . G 7 HOH A 4 504 38 HOH HOH . G 7 HOH A 5 505 106 HOH HOH . G 7 HOH A 6 506 108 HOH HOH . G 7 HOH A 7 507 113 HOH HOH . G 7 HOH A 8 508 23 HOH HOH . G 7 HOH A 9 509 115 HOH HOH . G 7 HOH A 10 510 35 HOH HOH . G 7 HOH A 11 511 125 HOH HOH . G 7 HOH A 12 512 87 HOH HOH . G 7 HOH A 13 513 120 HOH HOH . G 7 HOH A 14 514 26 HOH HOH . G 7 HOH A 15 515 60 HOH HOH . G 7 HOH A 16 516 95 HOH HOH . G 7 HOH A 17 517 67 HOH HOH . G 7 HOH A 18 518 27 HOH HOH . G 7 HOH A 19 519 99 HOH HOH . G 7 HOH A 20 520 21 HOH HOH . G 7 HOH A 21 521 128 HOH HOH . G 7 HOH A 22 522 22 HOH HOH . G 7 HOH A 23 523 74 HOH HOH . G 7 HOH A 24 524 58 HOH HOH . G 7 HOH A 25 525 15 HOH HOH . G 7 HOH A 26 526 83 HOH HOH . G 7 HOH A 27 527 34 HOH HOH . G 7 HOH A 28 528 75 HOH HOH . G 7 HOH A 29 529 116 HOH HOH . G 7 HOH A 30 530 77 HOH HOH . G 7 HOH A 31 531 78 HOH HOH . G 7 HOH A 32 532 18 HOH HOH . G 7 HOH A 33 533 65 HOH HOH . G 7 HOH A 34 534 109 HOH HOH . G 7 HOH A 35 535 19 HOH HOH . G 7 HOH A 36 536 5 HOH HOH . G 7 HOH A 37 537 54 HOH HOH . G 7 HOH A 38 538 49 HOH HOH . G 7 HOH A 39 539 33 HOH HOH . G 7 HOH A 40 540 1 HOH HOH . G 7 HOH A 41 541 124 HOH HOH . G 7 HOH A 42 542 3 HOH HOH . G 7 HOH A 43 543 25 HOH HOH . G 7 HOH A 44 544 80 HOH HOH . G 7 HOH A 45 545 102 HOH HOH . G 7 HOH A 46 546 81 HOH HOH . G 7 HOH A 47 547 28 HOH HOH . G 7 HOH A 48 548 62 HOH HOH . G 7 HOH A 49 549 44 HOH HOH . G 7 HOH A 50 550 112 HOH HOH . G 7 HOH A 51 551 20 HOH HOH . G 7 HOH A 52 552 86 HOH HOH . G 7 HOH A 53 553 41 HOH HOH . G 7 HOH A 54 554 42 HOH HOH . G 7 HOH A 55 555 37 HOH HOH . G 7 HOH A 56 556 70 HOH HOH . G 7 HOH A 57 557 71 HOH HOH . G 7 HOH A 58 558 4 HOH HOH . G 7 HOH A 59 559 88 HOH HOH . G 7 HOH A 60 560 73 HOH HOH . G 7 HOH A 61 561 52 HOH HOH . G 7 HOH A 62 562 91 HOH HOH . G 7 HOH A 63 563 94 HOH HOH . G 7 HOH A 64 564 69 HOH HOH . G 7 HOH A 65 565 90 HOH HOH . G 7 HOH A 66 566 129 HOH HOH . G 7 HOH A 67 567 63 HOH HOH . G 7 HOH A 68 568 119 HOH HOH . G 7 HOH A 69 569 84 HOH HOH . G 7 HOH A 70 570 97 HOH HOH . G 7 HOH A 71 571 79 HOH HOH . G 7 HOH A 72 572 56 HOH HOH . G 7 HOH A 73 573 114 HOH HOH . G 7 HOH A 74 574 32 HOH HOH . G 7 HOH A 75 575 50 HOH HOH . G 7 HOH A 76 576 82 HOH HOH . G 7 HOH A 77 577 104 HOH HOH . G 7 HOH A 78 578 121 HOH HOH . G 7 HOH A 79 579 111 HOH HOH . G 7 HOH A 80 580 61 HOH HOH . G 7 HOH A 81 581 46 HOH HOH . G 7 HOH A 82 582 85 HOH HOH . G 7 HOH A 83 583 118 HOH HOH . G 7 HOH A 84 584 123 HOH HOH . G 7 HOH A 85 585 59 HOH HOH . G 7 HOH A 86 586 29 HOH HOH . G 7 HOH A 87 587 122 HOH HOH . G 7 HOH A 88 588 98 HOH HOH . G 7 HOH A 89 589 10 HOH HOH . G 7 HOH A 90 590 57 HOH HOH . G 7 HOH A 91 591 9 HOH HOH . G 7 HOH A 92 592 14 HOH HOH . G 7 HOH A 93 593 55 HOH HOH . G 7 HOH A 94 594 48 HOH HOH . G 7 HOH A 95 595 51 HOH HOH . G 7 HOH A 96 596 72 HOH HOH . G 7 HOH A 97 597 126 HOH HOH . G 7 HOH A 98 598 103 HOH HOH . G 7 HOH A 99 599 101 HOH HOH . G 7 HOH A 100 600 130 HOH HOH . G 7 HOH A 101 601 53 HOH HOH . G 7 HOH A 102 602 45 HOH HOH . G 7 HOH A 103 603 6 HOH HOH . G 7 HOH A 104 604 11 HOH HOH . G 7 HOH A 105 605 31 HOH HOH . G 7 HOH A 106 606 13 HOH HOH . G 7 HOH A 107 607 47 HOH HOH . G 7 HOH A 108 608 89 HOH HOH . G 7 HOH A 109 609 66 HOH HOH . G 7 HOH A 110 610 2 HOH HOH . G 7 HOH A 111 611 36 HOH HOH . G 7 HOH A 112 612 8 HOH HOH . G 7 HOH A 113 613 117 HOH HOH . G 7 HOH A 114 614 30 HOH HOH . G 7 HOH A 115 615 105 HOH HOH . G 7 HOH A 116 616 100 HOH HOH . G 7 HOH A 117 617 7 HOH HOH . G 7 HOH A 118 618 76 HOH HOH . G 7 HOH A 119 619 17 HOH HOH . G 7 HOH A 120 620 110 HOH HOH . G 7 HOH A 121 621 107 HOH HOH . G 7 HOH A 122 622 127 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 . . . F 6 24.263 91.512 -3.766 1 41.54 ? PB ADP 405 A 1 HETATM 2 O O1B ADP . . . F 6 23.635 90.754 -4.953 1 41.21 ? O1B ADP 405 A 1 HETATM 3 O O2B ADP . . . F 6 25.573 92.078 -4.188 1 42.6 ? O2B ADP 405 A 1 HETATM 4 O O3B ADP . . . F 6 23.321 92.644 -3.353 1 38.99 ? O3B ADP 405 A 1 HETATM 5 P PA ADP . . . F 6 24.075 90.669 -0.955 1 35.21 ? PA ADP 405 A 1 HETATM 6 O O1A ADP . . . F 6 23.463 92.077 -0.683 1 33.15 ? O1A ADP 405 A 1 HETATM 7 O O2A ADP . . . F 6 25.276 90.469 -0.1 1 33.49 ? O2A ADP 405 A 1 HETATM 8 O O3A ADP . . . F 6 24.465 90.543 -2.506 1 41.32 ? O3A ADP 405 A 1 HETATM 9 O O5' ADP . . . F 6 22.945 89.513 -0.576 1 35.95 ? O5' ADP 405 A 1 HETATM 10 C C5' ADP . . . F 6 21.763 89.462 -1.345 1 36.4 ? C5' ADP 405 A 1 HETATM 11 C C4' ADP . . . F 6 20.598 89.06 -0.478 1 39.36 ? C4' ADP 405 A 1 HETATM 12 O O4' ADP . . . F 6 20.857 87.782 0.158 1 39.31 ? O4' ADP 405 A 1 HETATM 13 C C3' ADP . . . F 6 20.449 90.061 0.663 1 43.33 ? C3' ADP 405 A 1 HETATM 14 O O3' ADP . . . F 6 19.555 91.117 0.3 1 45.48 ? O3' ADP 405 A 1 HETATM 15 C C2' ADP . . . F 6 19.862 89.184 1.762 1 42.51 ? C2' ADP 405 A 1 HETATM 16 O O2' ADP . . . F 6 18.442 89.134 1.617 1 40.06 ? O2' ADP 405 A 1 HETATM 17 C C1' ADP . . . F 6 20.446 87.791 1.509 1 41.25 ? C1' ADP 405 A 1 HETATM 18 N N9 ADP . . . F 6 21.494 87.551 2.307 1 39.09 ? N9 ADP 405 A 1 HETATM 19 C C8 ADP . . . F 6 22.776 87.949 2.091 1 37.77 ? C8 ADP 405 A 1 HETATM 20 N N7 ADP . . . F 6 23.553 87.518 3.108 1 35.51 ? N7 ADP 405 A 1 HETATM 21 C C5 ADP . . . F 6 22.765 86.844 3.971 1 33.96 ? C5 ADP 405 A 1 HETATM 22 C C6 ADP . . . F 6 23.019 86.188 5.182 1 33.52 ? C6 ADP 405 A 1 HETATM 23 N N6 ADP . . . F 6 24.25 86.152 5.698 1 30.54 ? N6 ADP 405 A 1 HETATM 24 N N1 ADP . . . F 6 22.009 85.584 5.84 1 34.57 ? N1 ADP 405 A 1 HETATM 25 C C2 ADP . . . F 6 20.777 85.642 5.293 1 36.12 ? C2 ADP 405 A 1 HETATM 26 N N3 ADP . . . F 6 20.481 86.245 4.157 1 38.1 ? N3 ADP 405 A 1 HETATM 27 C C4 ADP . . . F 6 21.466 86.862 3.469 1 36.87 ? C4 ADP 405 A 1 HETATM 28 H "H5'1" ADP . . . F 6 21.872 88.813 -2.059 1 43.68 ? "H5'1" ADP 405 A 1 HETATM 29 H "H5'2" ADP . . . F 6 21.59 90.336 -1.729 1 43.68 ? "H5'2" ADP 405 A 1 HETATM 30 H H4' ADP . . . F 6 19.78 89.019 -0.997 1 47.23 ? H4' ADP 405 A 1 HETATM 31 H H3' ADP . . . F 6 21.314 90.409 0.931 1 52 ? H3' ADP 405 A 1 HETATM 32 H HO3' ADP . . . F 6 19.415 91.615 0.975 1 54.58 ? HO3' ADP 405 A 1 HETATM 33 H H2' ADP . . . F 6 20.115 89.514 2.638 1 51.01 ? H2' ADP 405 A 1 HETATM 34 H HO2' ADP . . . F 6 18.112 89.902 1.77 1 48.08 ? HO2' ADP 405 A 1 HETATM 35 H H1' ADP . . . F 6 19.761 87.119 1.649 1 49.49 ? H1' ADP 405 A 1 HETATM 36 H H8 ADP . . . F 6 23.071 88.442 1.36 1 45.32 ? H8 ADP 405 A 1 HETATM 37 H HN61 ADP . . . F 6 24.393 85.745 6.442 1 36.64 ? HN61 ADP 405 A 1 HETATM 38 H HN62 ADP . . . F 6 24.9 86.536 5.286 1 36.64 ? HN62 ADP 405 A 1 HETATM 39 H H2 ADP . . . F 6 20.083 85.225 5.752 1 43.34 ? H2 ADP 405 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #