data_2DPY # _model_server_result.job_id uLezG66lM1TKnrEvS3wQ4A _model_server_result.datetime_utc '2025-03-05 02:53:24' _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 2dpy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":600}' # _entry.id 2DPY # _exptl.entry_id 2DPY _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 94.13 _cell.angle_gamma 90 _cell.entry_id 2DPY _cell.length_a 48.16 _cell.length_b 72.75 _cell.length_c 125.74 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DPY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D 1 1 B,C,E 2 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 C _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 2DPY _atom_sites.fract_transf_matrix[1][1] 0.020764 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001499 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013746 _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] 0.007974 _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 C 2 ADP B 1 600 600 ADP ADP . D 3 HOH A 1 457 1 HOH WAT . D 3 HOH A 2 458 2 HOH WAT . D 3 HOH A 3 459 3 HOH WAT . D 3 HOH A 4 460 4 HOH WAT . D 3 HOH A 5 461 7 HOH WAT . D 3 HOH A 6 462 9 HOH WAT . D 3 HOH A 7 463 10 HOH WAT . D 3 HOH A 8 464 13 HOH WAT . D 3 HOH A 9 465 14 HOH WAT . D 3 HOH A 10 466 17 HOH WAT . D 3 HOH A 11 467 18 HOH WAT . D 3 HOH A 12 468 22 HOH WAT . D 3 HOH A 13 469 23 HOH WAT . D 3 HOH A 14 470 24 HOH WAT . D 3 HOH A 15 471 25 HOH WAT . D 3 HOH A 16 472 26 HOH WAT . D 3 HOH A 17 473 27 HOH WAT . D 3 HOH A 18 474 28 HOH WAT . D 3 HOH A 19 475 29 HOH WAT . D 3 HOH A 20 476 30 HOH WAT . D 3 HOH A 21 477 35 HOH WAT . D 3 HOH A 22 478 36 HOH WAT . D 3 HOH A 23 479 37 HOH WAT . D 3 HOH A 24 480 38 HOH WAT . D 3 HOH A 25 481 39 HOH WAT . D 3 HOH A 26 482 41 HOH WAT . D 3 HOH A 27 483 42 HOH WAT . D 3 HOH A 28 484 44 HOH WAT . D 3 HOH A 29 485 45 HOH WAT . D 3 HOH A 30 486 47 HOH WAT . D 3 HOH A 31 487 48 HOH WAT . D 3 HOH A 32 488 49 HOH WAT . D 3 HOH A 33 489 51 HOH WAT . D 3 HOH A 34 490 53 HOH WAT . D 3 HOH A 35 491 59 HOH WAT . D 3 HOH A 36 492 60 HOH WAT . D 3 HOH A 37 493 63 HOH WAT . D 3 HOH A 38 494 64 HOH WAT . D 3 HOH A 39 495 67 HOH WAT . D 3 HOH A 40 496 69 HOH WAT . D 3 HOH A 41 497 71 HOH WAT . D 3 HOH A 42 498 75 HOH WAT . D 3 HOH A 43 499 76 HOH WAT . D 3 HOH A 44 500 77 HOH WAT . D 3 HOH A 45 501 81 HOH WAT . D 3 HOH A 46 502 86 HOH WAT . D 3 HOH A 47 503 87 HOH WAT . D 3 HOH A 48 504 90 HOH WAT . D 3 HOH A 49 505 92 HOH WAT . D 3 HOH A 50 506 93 HOH WAT . D 3 HOH A 51 507 94 HOH WAT . D 3 HOH A 52 508 96 HOH WAT . D 3 HOH A 53 509 99 HOH WAT . D 3 HOH A 54 510 100 HOH WAT . D 3 HOH A 55 511 102 HOH WAT . D 3 HOH A 56 512 103 HOH WAT . D 3 HOH A 57 513 106 HOH WAT . D 3 HOH A 58 514 110 HOH WAT . D 3 HOH A 59 515 111 HOH WAT . D 3 HOH A 60 516 112 HOH WAT . D 3 HOH A 61 517 114 HOH WAT . D 3 HOH A 62 518 115 HOH WAT . D 3 HOH A 63 519 116 HOH WAT . D 3 HOH A 64 520 121 HOH WAT . D 3 HOH A 65 521 122 HOH WAT . D 3 HOH A 66 522 123 HOH WAT . D 3 HOH A 67 523 125 HOH WAT . D 3 HOH A 68 524 126 HOH WAT . D 3 HOH A 69 525 127 HOH WAT . D 3 HOH A 70 526 129 HOH WAT . D 3 HOH A 71 527 130 HOH WAT . E 3 HOH B 1 601 5 HOH WAT . E 3 HOH B 2 602 6 HOH WAT . E 3 HOH B 3 603 8 HOH WAT . E 3 HOH B 4 604 11 HOH WAT . E 3 HOH B 5 605 12 HOH WAT . E 3 HOH B 6 606 15 HOH WAT . E 3 HOH B 7 607 16 HOH WAT . E 3 HOH B 8 608 19 HOH WAT . E 3 HOH B 9 609 20 HOH WAT . E 3 HOH B 10 610 21 HOH WAT . E 3 HOH B 11 611 31 HOH WAT . E 3 HOH B 12 612 32 HOH WAT . E 3 HOH B 13 613 33 HOH WAT . E 3 HOH B 14 614 34 HOH WAT . E 3 HOH B 15 615 40 HOH WAT . E 3 HOH B 16 616 43 HOH WAT . E 3 HOH B 17 617 46 HOH WAT . E 3 HOH B 18 618 50 HOH WAT . E 3 HOH B 19 619 52 HOH WAT . E 3 HOH B 20 620 54 HOH WAT . E 3 HOH B 21 621 55 HOH WAT . E 3 HOH B 22 622 56 HOH WAT . E 3 HOH B 23 623 57 HOH WAT . E 3 HOH B 24 624 58 HOH WAT . E 3 HOH B 25 625 61 HOH WAT . E 3 HOH B 26 626 62 HOH WAT . E 3 HOH B 27 627 65 HOH WAT . E 3 HOH B 28 628 66 HOH WAT . E 3 HOH B 29 629 68 HOH WAT . E 3 HOH B 30 630 70 HOH WAT . E 3 HOH B 31 631 72 HOH WAT . E 3 HOH B 32 632 73 HOH WAT . E 3 HOH B 33 633 74 HOH WAT . E 3 HOH B 34 634 78 HOH WAT . E 3 HOH B 35 635 79 HOH WAT . E 3 HOH B 36 636 80 HOH WAT . E 3 HOH B 37 637 82 HOH WAT . E 3 HOH B 38 638 83 HOH WAT . E 3 HOH B 39 639 84 HOH WAT . E 3 HOH B 40 640 85 HOH WAT . E 3 HOH B 41 641 88 HOH WAT . E 3 HOH B 42 642 89 HOH WAT . E 3 HOH B 43 643 91 HOH WAT . E 3 HOH B 44 644 95 HOH WAT . E 3 HOH B 45 645 97 HOH WAT . E 3 HOH B 46 646 98 HOH WAT . E 3 HOH B 47 647 101 HOH WAT . E 3 HOH B 48 648 104 HOH WAT . E 3 HOH B 49 649 105 HOH WAT . E 3 HOH B 50 650 107 HOH WAT . E 3 HOH B 51 651 108 HOH WAT . E 3 HOH B 52 652 109 HOH WAT . E 3 HOH B 53 653 113 HOH WAT . E 3 HOH B 54 654 117 HOH WAT . E 3 HOH B 55 655 118 HOH WAT . E 3 HOH B 56 656 119 HOH WAT . E 3 HOH B 57 657 120 HOH WAT . E 3 HOH B 58 658 124 HOH WAT . E 3 HOH B 59 659 128 HOH WAT . E 3 HOH B 60 660 131 HOH WAT . E 3 HOH B 61 661 132 HOH WAT . E 3 HOH B 62 662 133 HOH WAT . # 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 . . . C 2 25.258 9.137 -33.685 1 133.24 ? PB ADP 600 B 1 HETATM 2 O O1B ADP . . . C 2 25.633 10.265 -34.593 1 133.13 ? O1B ADP 600 B 1 HETATM 3 O O2B ADP . . . C 2 25.933 9.3 -32.171 1 132.89 ? O2B ADP 600 B 1 HETATM 4 O O3B ADP . . . C 2 23.797 9.041 -33.531 1 132.72 ? O3B ADP 600 B 1 HETATM 5 P PA ADP . . . C 2 26.984 6.764 -33.768 1 133.62 ? PA ADP 600 B 1 HETATM 6 O O1A ADP . . . C 2 28.338 7.476 -34.008 1 133.45 ? O1A ADP 600 B 1 HETATM 7 O O2A ADP . . . C 2 26.909 6.319 -32.489 1 133.89 ? O2A ADP 600 B 1 HETATM 8 O O3A ADP . . . C 2 25.87 7.853 -34.233 1 133.67 ? O3A ADP 600 B 1 HETATM 9 O O5' ADP . . . C 2 26.676 5.696 -34.958 1 133.11 ? O5' ADP 600 B 1 HETATM 10 C C5' ADP . . . C 2 26.809 6.058 -36.31 1 131.8 ? C5' ADP 600 B 1 HETATM 11 C C4' ADP . . . C 2 26.93 4.826 -37.161 1 131.26 ? C4' ADP 600 B 1 HETATM 12 O O4' ADP . . . C 2 27.609 5.164 -38.398 1 131.21 ? O4' ADP 600 B 1 HETATM 13 C C3' ADP . . . C 2 27.801 3.719 -36.515 1 130.82 ? C3' ADP 600 B 1 HETATM 14 O O3' ADP . . . C 2 27.067 2.729 -35.81 1 130.19 ? O3' ADP 600 B 1 HETATM 15 C C2' ADP . . . C 2 28.526 3.069 -37.749 1 130.7 ? C2' ADP 600 B 1 HETATM 16 O O2' ADP . . . C 2 27.706 2.11 -38.337 1 130.94 ? O2' ADP 600 B 1 HETATM 17 C C1' ADP . . . C 2 28.778 4.295 -38.62 1 130.79 ? C1' ADP 600 B 1 HETATM 18 N N9 ADP . . . C 2 30.173 4.999 -38.281 1 130.21 ? N9 ADP 600 B 1 HETATM 19 C C8 ADP . . . C 2 30.309 6.099 -37.558 1 130.19 ? C8 ADP 600 B 1 HETATM 20 N N7 ADP . . . C 2 31.602 6.418 -37.477 1 130.11 ? N7 ADP 600 B 1 HETATM 21 C C5 ADP . . . C 2 32.296 5.544 -38.15 1 129.52 ? C5 ADP 600 B 1 HETATM 22 C C6 ADP . . . C 2 33.662 5.368 -38.413 1 128.99 ? C6 ADP 600 B 1 HETATM 23 N N6 ADP . . . C 2 34.589 6.238 -37.929 1 127.87 ? N6 ADP 600 B 1 HETATM 24 N N1 ADP . . . C 2 34.122 4.337 -39.179 1 129.08 ? N1 ADP 600 B 1 HETATM 25 C C2 ADP . . . C 2 33.213 3.428 -39.686 1 129.44 ? C2 ADP 600 B 1 HETATM 26 N N3 ADP . . . C 2 31.868 3.572 -39.427 1 129.57 ? N3 ADP 600 B 1 HETATM 27 C C4 ADP . . . C 2 31.393 4.616 -38.661 1 129.74 ? C4 ADP 600 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #