data_5GRF # _model_server_result.job_id OmaRr053JDNpi116P3wNDA _model_server_result.datetime_utc '2024-11-05 01:00:03' _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 5grf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5GRF # _exptl.entry_id 5GRF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 120 _cell.entry_id 5GRF _cell.length_a 114.336 _cell.length_b 114.336 _cell.length_c 143.901 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GRF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 4 _struct_asym.id D _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 O ARG 272 B ARG 272 1_555 E MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc2 C O6 CIT . B CIT 401 1_555 E MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 D O2B ADP . B ADP 402 1_555 E MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 E MG MG . B MG 403 1_555 G O HOH . B HOH 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? metalc ? metalc5 E MG MG . B MG 403 1_555 G O HOH . B HOH 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? # _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 5GRF _atom_sites.fract_transf_matrix[1][1] 0.008746 _atom_sites.fract_transf_matrix[1][2] 0.00505 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010099 _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] 0.006949 _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 3 CIT B 1 401 1 CIT CIT . D 4 ADP B 1 402 1 ADP ADP . E 5 MG B 1 403 1 MG MG . F 6 HOH A 1 401 4 HOH HOH . F 6 HOH A 2 402 11 HOH HOH . F 6 HOH A 3 403 40 HOH HOH . F 6 HOH A 4 404 77 HOH HOH . F 6 HOH A 5 405 58 HOH HOH . F 6 HOH A 6 406 128 HOH HOH . F 6 HOH A 7 407 12 HOH HOH . F 6 HOH A 8 408 41 HOH HOH . F 6 HOH A 9 409 82 HOH HOH . F 6 HOH A 10 410 64 HOH HOH . F 6 HOH A 11 411 96 HOH HOH . F 6 HOH A 12 412 9 HOH HOH . F 6 HOH A 13 413 73 HOH HOH . F 6 HOH A 14 414 117 HOH HOH . F 6 HOH A 15 415 114 HOH HOH . F 6 HOH A 16 416 91 HOH HOH . F 6 HOH A 17 417 108 HOH HOH . F 6 HOH A 18 418 68 HOH HOH . F 6 HOH A 19 419 98 HOH HOH . F 6 HOH A 20 420 85 HOH HOH . F 6 HOH A 21 421 75 HOH HOH . F 6 HOH A 22 422 71 HOH HOH . F 6 HOH A 23 423 56 HOH HOH . F 6 HOH A 24 424 109 HOH HOH . G 6 HOH B 1 501 21 HOH HOH . G 6 HOH B 2 502 90 HOH HOH . G 6 HOH B 3 503 88 HOH HOH . G 6 HOH B 4 504 28 HOH HOH . G 6 HOH B 5 505 112 HOH HOH . G 6 HOH B 6 506 37 HOH HOH . G 6 HOH B 7 507 36 HOH HOH . G 6 HOH B 8 508 13 HOH HOH . G 6 HOH B 9 509 18 HOH HOH . G 6 HOH B 10 510 99 HOH HOH . G 6 HOH B 11 511 22 HOH HOH . G 6 HOH B 12 512 93 HOH HOH . G 6 HOH B 13 513 5 HOH HOH . G 6 HOH B 14 514 57 HOH HOH . G 6 HOH B 15 515 42 HOH HOH . G 6 HOH B 16 516 38 HOH HOH . G 6 HOH B 17 517 6 HOH HOH . G 6 HOH B 18 518 27 HOH HOH . G 6 HOH B 19 519 131 HOH HOH . G 6 HOH B 20 520 10 HOH HOH . G 6 HOH B 21 521 30 HOH HOH . G 6 HOH B 22 522 124 HOH HOH . G 6 HOH B 23 523 7 HOH HOH . G 6 HOH B 24 524 49 HOH HOH . G 6 HOH B 25 525 53 HOH HOH . G 6 HOH B 26 526 54 HOH HOH . G 6 HOH B 27 527 69 HOH HOH . G 6 HOH B 28 528 66 HOH HOH . G 6 HOH B 29 529 23 HOH HOH . G 6 HOH B 30 530 130 HOH HOH . G 6 HOH B 31 531 52 HOH HOH . G 6 HOH B 32 532 132 HOH HOH . G 6 HOH B 33 533 43 HOH HOH . G 6 HOH B 34 534 102 HOH HOH . G 6 HOH B 35 535 31 HOH HOH . G 6 HOH B 36 536 110 HOH HOH . G 6 HOH B 37 537 63 HOH HOH . G 6 HOH B 38 538 81 HOH HOH . G 6 HOH B 39 539 39 HOH HOH . G 6 HOH B 40 540 24 HOH HOH . G 6 HOH B 41 541 8 HOH HOH . G 6 HOH B 42 542 19 HOH HOH . G 6 HOH B 43 543 97 HOH HOH . G 6 HOH B 44 544 100 HOH HOH . G 6 HOH B 45 545 84 HOH HOH . G 6 HOH B 46 546 129 HOH HOH . G 6 HOH B 47 547 26 HOH HOH . G 6 HOH B 48 548 55 HOH HOH . G 6 HOH B 49 549 29 HOH HOH . G 6 HOH B 50 550 62 HOH HOH . G 6 HOH B 51 551 111 HOH HOH . G 6 HOH B 52 552 48 HOH HOH . G 6 HOH B 53 553 95 HOH HOH . G 6 HOH B 54 554 61 HOH HOH . G 6 HOH B 55 555 14 HOH HOH . G 6 HOH B 56 556 33 HOH HOH . G 6 HOH B 57 557 20 HOH HOH . G 6 HOH B 58 558 51 HOH HOH . G 6 HOH B 59 559 25 HOH HOH . G 6 HOH B 60 560 65 HOH HOH . G 6 HOH B 61 561 115 HOH HOH . G 6 HOH B 62 562 15 HOH HOH . G 6 HOH B 63 563 44 HOH HOH . G 6 HOH B 64 564 45 HOH HOH . G 6 HOH B 65 565 133 HOH HOH . G 6 HOH B 66 566 3 HOH HOH . G 6 HOH B 67 567 2 HOH HOH . G 6 HOH B 68 568 47 HOH HOH . G 6 HOH B 69 569 35 HOH HOH . G 6 HOH B 70 570 76 HOH HOH . G 6 HOH B 71 571 67 HOH HOH . G 6 HOH B 72 572 34 HOH HOH . G 6 HOH B 73 573 70 HOH HOH . G 6 HOH B 74 574 103 HOH HOH . G 6 HOH B 75 575 116 HOH HOH . G 6 HOH B 76 576 50 HOH HOH . G 6 HOH B 77 577 134 HOH HOH . G 6 HOH B 78 578 89 HOH HOH . G 6 HOH B 79 579 126 HOH HOH . G 6 HOH B 80 580 46 HOH HOH . G 6 HOH B 81 581 32 HOH HOH . G 6 HOH B 82 582 107 HOH HOH . G 6 HOH B 83 583 80 HOH HOH . G 6 HOH B 84 584 78 HOH HOH . G 6 HOH B 85 585 1 HOH HOH . G 6 HOH B 86 586 127 HOH HOH . G 6 HOH B 87 587 94 HOH HOH . G 6 HOH B 88 588 16 HOH HOH . G 6 HOH B 89 589 72 HOH HOH . G 6 HOH B 90 590 104 HOH HOH . G 6 HOH B 91 591 122 HOH HOH . G 6 HOH B 92 592 121 HOH HOH . G 6 HOH B 93 593 101 HOH HOH . G 6 HOH B 94 594 106 HOH HOH . G 6 HOH B 95 595 113 HOH HOH . G 6 HOH B 96 596 120 HOH HOH . G 6 HOH B 97 597 79 HOH HOH . G 6 HOH B 98 598 74 HOH HOH . G 6 HOH B 99 599 59 HOH HOH . G 6 HOH B 100 600 92 HOH HOH . G 6 HOH B 101 601 87 HOH HOH . G 6 HOH B 102 602 118 HOH HOH . G 6 HOH B 103 603 119 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 4 41.973 -19.304 -0.717 1 121.09 ? PB ADP 402 B 1 HETATM 2 O O1B ADP . . . D 4 41.337 -19.647 -2.058 1 120.28 ? O1B ADP 402 B 1 HETATM 3 O O2B ADP . . . D 4 43.241 -18.54 -0.976 1 107.96 ? O2B ADP 402 B 1 HETATM 4 O O3B ADP . . . D 4 41.034 -18.437 0.128 1 108.81 ? O3B ADP 402 B 1 HETATM 5 P PA ADP . . . D 4 41.2 -21.751 0.625 1 72.26 ? PA ADP 402 B 1 HETATM 6 O O1A ADP . . . D 4 39.821 -21.174 0.544 1 94 ? O1A ADP 402 B 1 HETATM 7 O O2A ADP . . . D 4 41.505 -22.06 2.059 1 87.72 ? O2A ADP 402 B 1 HETATM 8 O O3A ADP . . . D 4 42.288 -20.677 0.082 1 119.2 ? O3A ADP 402 B 1 HETATM 9 O O5' ADP . . . D 4 41.253 -23.061 -0.236 1 84.61 ? O5' ADP 402 B 1 HETATM 10 C C5' ADP . . . D 4 42.289 -24.004 -0.061 1 84.41 ? C5' ADP 402 B 1 HETATM 11 C C4' ADP . . . D 4 41.739 -25.394 0.138 1 87.56 ? C4' ADP 402 B 1 HETATM 12 O O4' ADP . . . D 4 42.881 -26.349 0.23 1 88.61 ? O4' ADP 402 B 1 HETATM 13 C C3' ADP . . . D 4 41.015 -25.552 1.392 1 81.5 ? C3' ADP 402 B 1 HETATM 14 O O3' ADP . . . D 4 40.172 -26.749 1.267 1 71.3 ? O3' ADP 402 B 1 HETATM 15 C C2' ADP . . . D 4 42.022 -25.772 2.387 1 78.5 ? C2' ADP 402 B 1 HETATM 16 O O2' ADP . . . D 4 41.458 -26.415 3.599 1 76.32 ? O2' ADP 402 B 1 HETATM 17 C C1' ADP . . . D 4 42.994 -26.627 1.698 1 81.82 ? C1' ADP 402 B 1 HETATM 18 N N9 ADP . . . D 4 44.28 -26.37 2.154 1 76.33 ? N9 ADP 402 B 1 HETATM 19 C C8 ADP . . . D 4 45.092 -25.338 1.868 1 65.91 ? C8 ADP 402 B 1 HETATM 20 N N7 ADP . . . D 4 46.251 -25.458 2.529 1 67.81 ? N7 ADP 402 B 1 HETATM 21 C C5 ADP . . . D 4 46.215 -26.579 3.277 1 77 ? C5 ADP 402 B 1 HETATM 22 C C6 ADP . . . D 4 47.099 -27.224 4.166 1 74.24 ? C6 ADP 402 B 1 HETATM 23 N N6 ADP . . . D 4 48.372 -26.694 4.455 1 64.95 ? N6 ADP 402 B 1 HETATM 24 N N1 ADP . . . D 4 46.718 -28.376 4.752 1 76.64 ? N1 ADP 402 B 1 HETATM 25 C C2 ADP . . . D 4 45.511 -28.935 4.527 1 72.83 ? C2 ADP 402 B 1 HETATM 26 N N3 ADP . . . D 4 44.625 -28.341 3.668 1 69.02 ? N3 ADP 402 B 1 HETATM 27 C C4 ADP . . . D 4 44.952 -27.186 3.051 1 76.71 ? C4 ADP 402 B 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #