data_2YZL # _model_server_result.job_id OBsUXWZmXRD1WWNQ-wcpyw _model_server_result.datetime_utc '2024-10-18 19:33:06' _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 2yzl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 2YZL # _exptl.entry_id 2YZL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 2YZL _cell.length_a 82.31 _cell.length_b 82.31 _cell.length_c 85.21 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YZL _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1 A,B,C,D,E 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 2YZL _atom_sites.fract_transf_matrix[1][1] 0.012149 _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] 0.012149 _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] 0.011736 _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 SO4 A 1 511 511 SO4 SO4 . C 2 SO4 A 1 512 512 SO4 SO4 . D 3 ADP A 1 500 500 ADP ADP . E 4 HOH A 1 513 4 HOH HOH . E 4 HOH A 2 514 5 HOH HOH . E 4 HOH A 3 515 6 HOH HOH . E 4 HOH A 4 516 7 HOH HOH . E 4 HOH A 5 517 8 HOH HOH . E 4 HOH A 6 518 9 HOH HOH . E 4 HOH A 7 519 10 HOH HOH . E 4 HOH A 8 520 11 HOH HOH . E 4 HOH A 9 521 12 HOH HOH . E 4 HOH A 10 522 13 HOH HOH . E 4 HOH A 11 523 14 HOH HOH . E 4 HOH A 12 524 15 HOH HOH . E 4 HOH A 13 525 16 HOH HOH . E 4 HOH A 14 526 17 HOH HOH . E 4 HOH A 15 527 18 HOH HOH . E 4 HOH A 16 528 19 HOH HOH . E 4 HOH A 17 529 20 HOH HOH . E 4 HOH A 18 530 21 HOH HOH . E 4 HOH A 19 531 22 HOH HOH . E 4 HOH A 20 532 23 HOH HOH . E 4 HOH A 21 533 24 HOH HOH . E 4 HOH A 22 534 25 HOH HOH . E 4 HOH A 23 535 26 HOH HOH . E 4 HOH A 24 536 27 HOH HOH . E 4 HOH A 25 537 28 HOH HOH . E 4 HOH A 26 538 29 HOH HOH . E 4 HOH A 27 539 30 HOH HOH . E 4 HOH A 28 540 31 HOH HOH . E 4 HOH A 29 541 32 HOH HOH . E 4 HOH A 30 542 33 HOH HOH . E 4 HOH A 31 543 34 HOH HOH . E 4 HOH A 32 544 35 HOH HOH . E 4 HOH A 33 545 36 HOH HOH . E 4 HOH A 34 546 37 HOH HOH . E 4 HOH A 35 547 38 HOH HOH . E 4 HOH A 36 548 39 HOH HOH . E 4 HOH A 37 549 40 HOH HOH . E 4 HOH A 38 550 41 HOH HOH . E 4 HOH A 39 551 42 HOH HOH . E 4 HOH A 40 552 43 HOH HOH . E 4 HOH A 41 553 44 HOH HOH . E 4 HOH A 42 554 45 HOH HOH . E 4 HOH A 43 555 46 HOH HOH . E 4 HOH A 44 556 47 HOH HOH . E 4 HOH A 45 557 48 HOH HOH . E 4 HOH A 46 558 49 HOH HOH . E 4 HOH A 47 559 50 HOH HOH . E 4 HOH A 48 560 51 HOH HOH . E 4 HOH A 49 561 52 HOH HOH . E 4 HOH A 50 562 53 HOH HOH . E 4 HOH A 51 563 54 HOH HOH . E 4 HOH A 52 564 55 HOH HOH . E 4 HOH A 53 565 56 HOH HOH . E 4 HOH A 54 566 57 HOH HOH . E 4 HOH A 55 567 58 HOH HOH . E 4 HOH A 56 568 59 HOH HOH . E 4 HOH A 57 569 60 HOH HOH . E 4 HOH A 58 570 61 HOH HOH . E 4 HOH A 59 571 62 HOH HOH . E 4 HOH A 60 572 63 HOH HOH . E 4 HOH A 61 573 64 HOH HOH . E 4 HOH A 62 574 65 HOH HOH . E 4 HOH A 63 575 66 HOH HOH . E 4 HOH A 64 576 67 HOH HOH . E 4 HOH A 65 577 68 HOH HOH . E 4 HOH A 66 578 69 HOH HOH . E 4 HOH A 67 579 70 HOH HOH . E 4 HOH A 68 580 71 HOH HOH . E 4 HOH A 69 581 72 HOH HOH . E 4 HOH A 70 582 73 HOH HOH . E 4 HOH A 71 583 74 HOH HOH . E 4 HOH A 72 584 75 HOH HOH . E 4 HOH A 73 585 76 HOH HOH . E 4 HOH A 74 586 77 HOH HOH . E 4 HOH A 75 587 78 HOH HOH . E 4 HOH A 76 588 79 HOH HOH . E 4 HOH A 77 589 80 HOH HOH . E 4 HOH A 78 590 81 HOH HOH . E 4 HOH A 79 591 82 HOH HOH . E 4 HOH A 80 592 83 HOH HOH . E 4 HOH A 81 593 84 HOH HOH . E 4 HOH A 82 594 86 HOH HOH . E 4 HOH A 83 595 87 HOH HOH . E 4 HOH A 84 596 88 HOH HOH . E 4 HOH A 85 597 89 HOH HOH . E 4 HOH A 86 598 90 HOH HOH . E 4 HOH A 87 599 91 HOH HOH . E 4 HOH A 88 600 92 HOH HOH . E 4 HOH A 89 601 93 HOH HOH . E 4 HOH A 90 602 94 HOH HOH . E 4 HOH A 91 603 95 HOH HOH . E 4 HOH A 92 604 96 HOH HOH . E 4 HOH A 93 605 97 HOH HOH . E 4 HOH A 94 606 98 HOH HOH . E 4 HOH A 95 607 99 HOH HOH . E 4 HOH A 96 608 100 HOH HOH . E 4 HOH A 97 609 101 HOH HOH . E 4 HOH A 98 610 102 HOH HOH . E 4 HOH A 99 611 103 HOH HOH . E 4 HOH A 100 612 104 HOH HOH . E 4 HOH A 101 613 106 HOH HOH . E 4 HOH A 102 614 107 HOH HOH . E 4 HOH A 103 615 108 HOH HOH . E 4 HOH A 104 616 109 HOH HOH . E 4 HOH A 105 617 110 HOH HOH . E 4 HOH A 106 618 112 HOH HOH . E 4 HOH A 107 619 113 HOH HOH . E 4 HOH A 108 620 114 HOH HOH . E 4 HOH A 109 621 115 HOH HOH . E 4 HOH A 110 622 116 HOH HOH . E 4 HOH A 111 623 117 HOH HOH . E 4 HOH A 112 624 118 HOH HOH . E 4 HOH A 113 625 119 HOH HOH . E 4 HOH A 114 626 120 HOH HOH . E 4 HOH A 115 627 121 HOH HOH . E 4 HOH A 116 628 122 HOH HOH . E 4 HOH A 117 629 123 HOH HOH . E 4 HOH A 118 630 124 HOH HOH . E 4 HOH A 119 631 125 HOH HOH . E 4 HOH A 120 632 126 HOH HOH . E 4 HOH A 121 633 127 HOH HOH . E 4 HOH A 122 634 128 HOH HOH . E 4 HOH A 123 635 129 HOH HOH . E 4 HOH A 124 636 130 HOH HOH . E 4 HOH A 125 637 131 HOH HOH . E 4 HOH A 126 638 132 HOH HOH . E 4 HOH A 127 639 133 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 . . . D 3 35.414 27.77 19.942 1 34.77 ? PB ADP 500 A 1 HETATM 2 O O1B ADP . . . D 3 35.913 26.617 20.7 1 38.2 ? O1B ADP 500 A 1 HETATM 3 O O2B ADP . . . D 3 35.347 29.272 20.488 1 37.24 ? O2B ADP 500 A 1 HETATM 4 O O3B ADP . . . D 3 34.442 27.476 18.678 1 36.6 ? O3B ADP 500 A 1 HETATM 5 P PA ADP . . . D 3 33.966 28.183 22.323 1 32.99 ? PA ADP 500 A 1 HETATM 6 O O1A ADP . . . D 3 32.662 28.11 23.012 1 31.32 ? O1A ADP 500 A 1 HETATM 7 O O2A ADP . . . D 3 35.33 28.532 23.081 1 30.24 ? O2A ADP 500 A 1 HETATM 8 O O3A ADP . . . D 3 34.05 27.438 20.836 1 35.47 ? O3A ADP 500 A 1 HETATM 9 O O5' ADP . . . D 3 34.297 26.722 23.004 1 31.63 ? O5' ADP 500 A 1 HETATM 10 C C5' ADP . . . D 3 33.264 25.742 22.769 1 33.24 ? C5' ADP 500 A 1 HETATM 11 C C4' ADP . . . D 3 33.919 24.403 22.465 1 33.48 ? C4' ADP 500 A 1 HETATM 12 O O4' ADP . . . D 3 33.413 23.368 23.365 1 30.93 ? O4' ADP 500 A 1 HETATM 13 C C3' ADP . . . D 3 33.608 23.963 21.029 1 33.97 ? C3' ADP 500 A 1 HETATM 14 O O3' ADP . . . D 3 34.815 23.531 20.382 1 36.05 ? O3' ADP 500 A 1 HETATM 15 C C2' ADP . . . D 3 32.58 22.845 21.208 1 32.45 ? C2' ADP 500 A 1 HETATM 16 O O2' ADP . . . D 3 32.644 21.924 20.128 1 34.74 ? O2' ADP 500 A 1 HETATM 17 C C1' ADP . . . D 3 32.97 22.237 22.566 1 29.37 ? C1' ADP 500 A 1 HETATM 18 N N9 ADP . . . D 3 31.829 21.568 23.243 1 26.36 ? N9 ADP 500 A 1 HETATM 19 C C8 ADP . . . D 3 30.551 22.055 23.412 1 26.12 ? C8 ADP 500 A 1 HETATM 20 N N7 ADP . . . D 3 29.816 21.195 24.07 1 24.4 ? N7 ADP 500 A 1 HETATM 21 C C5 ADP . . . D 3 30.559 20.094 24.351 1 25.55 ? C5 ADP 500 A 1 HETATM 22 C C6 ADP . . . D 3 30.326 18.836 24.996 1 25.38 ? C6 ADP 500 A 1 HETATM 23 N N6 ADP . . . D 3 29.176 18.609 25.732 1 23.26 ? N6 ADP 500 A 1 HETATM 24 N N1 ADP . . . D 3 31.264 17.869 24.872 1 25.96 ? N1 ADP 500 A 1 HETATM 25 C C2 ADP . . . D 3 32.489 18.145 24.41 1 27.12 ? C2 ADP 500 A 1 HETATM 26 N N3 ADP . . . D 3 32.811 19.373 23.991 1 24.63 ? N3 ADP 500 A 1 HETATM 27 C C4 ADP . . . D 3 31.867 20.328 23.84 1 25.75 ? C4 ADP 500 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #