data_3RFC # _model_server_result.job_id J4sSop9PRMFooP7gz-KdGg _model_server_result.datetime_utc '2025-03-20 23:32:41' _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 3rfc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":368}' # _entry.id 3RFC # _exptl.entry_id 3RFC _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 3RFC _cell.length_a 83.236 _cell.length_b 83.236 _cell.length_c 98.277 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RFC _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 49.1385 # _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 319 A ASP 302 1_555 C MG MG . A MG 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc2 B O1A ADP . A ADP 368 1_555 C MG MG . A MG 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc3 C MG MG . A MG 369 1_555 D O HOH . A HOH 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? # _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 3RFC _atom_sites.fract_transf_matrix[1][1] 0.012014 _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] 0.012014 _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] 0.010175 _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 1 368 1 ADP ADP . C 3 MG A 1 369 1 MG MG . D 4 HOH A 1 370 1 HOH HOH . D 4 HOH A 2 371 2 HOH HOH . D 4 HOH A 3 372 3 HOH HOH . D 4 HOH A 4 373 4 HOH HOH . D 4 HOH A 5 374 5 HOH HOH . D 4 HOH A 6 375 6 HOH HOH . D 4 HOH A 7 376 7 HOH HOH . D 4 HOH A 8 377 8 HOH HOH . D 4 HOH A 9 378 9 HOH HOH . D 4 HOH A 10 379 10 HOH HOH . D 4 HOH A 11 380 11 HOH HOH . D 4 HOH A 12 381 12 HOH HOH . D 4 HOH A 13 382 13 HOH HOH . D 4 HOH A 14 383 14 HOH HOH . D 4 HOH A 15 384 15 HOH HOH . D 4 HOH A 16 385 16 HOH HOH . D 4 HOH A 17 386 17 HOH HOH . D 4 HOH A 18 387 18 HOH HOH . D 4 HOH A 19 388 19 HOH HOH . D 4 HOH A 20 389 20 HOH HOH . D 4 HOH A 21 390 21 HOH HOH . D 4 HOH A 22 391 22 HOH HOH . D 4 HOH A 23 392 23 HOH HOH . D 4 HOH A 24 393 24 HOH HOH . D 4 HOH A 25 394 25 HOH HOH . D 4 HOH A 26 395 26 HOH HOH . D 4 HOH A 27 396 27 HOH HOH . D 4 HOH A 28 397 28 HOH HOH . D 4 HOH A 29 398 29 HOH HOH . D 4 HOH A 30 399 30 HOH HOH . D 4 HOH A 31 400 31 HOH HOH . D 4 HOH A 32 401 32 HOH HOH . D 4 HOH A 33 402 33 HOH HOH . D 4 HOH A 34 403 34 HOH HOH . D 4 HOH A 35 404 35 HOH HOH . D 4 HOH A 36 405 36 HOH HOH . D 4 HOH A 37 406 37 HOH HOH . D 4 HOH A 38 407 38 HOH HOH . D 4 HOH A 39 408 39 HOH HOH . D 4 HOH A 40 409 40 HOH HOH . D 4 HOH A 41 410 41 HOH HOH . D 4 HOH A 42 411 42 HOH HOH . D 4 HOH A 43 412 43 HOH HOH . D 4 HOH A 44 413 44 HOH HOH . D 4 HOH A 45 414 45 HOH HOH . D 4 HOH A 46 415 46 HOH HOH . D 4 HOH A 47 416 47 HOH HOH . D 4 HOH A 48 417 48 HOH HOH . D 4 HOH A 49 418 49 HOH HOH . D 4 HOH A 50 419 50 HOH HOH . D 4 HOH A 51 420 51 HOH HOH . D 4 HOH A 52 421 52 HOH HOH . D 4 HOH A 53 422 53 HOH HOH . D 4 HOH A 54 423 54 HOH HOH . D 4 HOH A 55 424 55 HOH HOH . D 4 HOH A 56 425 56 HOH HOH . D 4 HOH A 57 426 57 HOH HOH . D 4 HOH A 58 427 58 HOH HOH . D 4 HOH A 59 428 59 HOH HOH . D 4 HOH A 60 429 60 HOH HOH . D 4 HOH A 61 430 61 HOH HOH . D 4 HOH A 62 431 62 HOH HOH . D 4 HOH A 63 432 63 HOH HOH . D 4 HOH A 64 433 64 HOH HOH . D 4 HOH A 65 434 65 HOH HOH . D 4 HOH A 66 435 66 HOH HOH . D 4 HOH A 67 436 67 HOH HOH . D 4 HOH A 68 437 68 HOH HOH . D 4 HOH A 69 438 69 HOH HOH . D 4 HOH A 70 439 70 HOH HOH . D 4 HOH A 71 440 71 HOH HOH . D 4 HOH A 72 441 72 HOH HOH . D 4 HOH A 73 442 73 HOH HOH . D 4 HOH A 74 443 74 HOH HOH . D 4 HOH A 75 444 75 HOH HOH . D 4 HOH A 76 445 76 HOH HOH . D 4 HOH A 77 446 77 HOH HOH . D 4 HOH A 78 447 78 HOH HOH . D 4 HOH A 79 448 79 HOH HOH . D 4 HOH A 80 449 80 HOH HOH . D 4 HOH A 81 450 81 HOH HOH . D 4 HOH A 82 451 82 HOH HOH . D 4 HOH A 83 452 83 HOH HOH . D 4 HOH A 84 453 84 HOH HOH . D 4 HOH A 85 454 85 HOH HOH . D 4 HOH A 86 455 86 HOH HOH . D 4 HOH A 87 456 87 HOH HOH . D 4 HOH A 88 457 88 HOH HOH . D 4 HOH A 89 458 89 HOH HOH . D 4 HOH A 90 459 90 HOH HOH . D 4 HOH A 91 460 91 HOH HOH . D 4 HOH A 92 461 92 HOH HOH . D 4 HOH A 93 462 93 HOH HOH . D 4 HOH A 94 463 94 HOH HOH . D 4 HOH A 95 464 95 HOH HOH . D 4 HOH A 96 465 96 HOH HOH . D 4 HOH A 97 466 97 HOH HOH . D 4 HOH A 98 467 98 HOH HOH . D 4 HOH A 99 468 99 HOH HOH . D 4 HOH A 100 469 100 HOH HOH . D 4 HOH A 101 470 101 HOH HOH . D 4 HOH A 102 471 102 HOH HOH . D 4 HOH A 103 472 103 HOH HOH . D 4 HOH A 104 473 104 HOH HOH . D 4 HOH A 105 474 105 HOH HOH . D 4 HOH A 106 475 106 HOH HOH . D 4 HOH A 107 476 107 HOH HOH . D 4 HOH A 108 477 108 HOH HOH . D 4 HOH A 109 478 109 HOH HOH . D 4 HOH A 110 479 110 HOH HOH . D 4 HOH A 111 480 111 HOH HOH . D 4 HOH A 112 481 112 HOH HOH . D 4 HOH A 113 482 113 HOH HOH . D 4 HOH A 114 483 114 HOH HOH . D 4 HOH A 115 484 115 HOH HOH . D 4 HOH A 116 485 116 HOH HOH . D 4 HOH A 117 486 117 HOH HOH . D 4 HOH A 118 487 118 HOH HOH . D 4 HOH A 119 488 119 HOH HOH . D 4 HOH A 120 489 120 HOH HOH . D 4 HOH A 121 490 121 HOH HOH . D 4 HOH A 122 491 122 HOH HOH . D 4 HOH A 123 492 123 HOH HOH . D 4 HOH A 124 493 124 HOH HOH . D 4 HOH A 125 494 125 HOH HOH . D 4 HOH A 126 495 126 HOH HOH . D 4 HOH A 127 496 127 HOH HOH . D 4 HOH A 128 497 128 HOH HOH . D 4 HOH A 129 498 129 HOH HOH . D 4 HOH A 130 499 130 HOH HOH . D 4 HOH A 131 500 131 HOH HOH . D 4 HOH A 132 501 132 HOH HOH . D 4 HOH A 133 502 133 HOH HOH . D 4 HOH A 134 503 134 HOH HOH . D 4 HOH A 135 504 135 HOH HOH . D 4 HOH A 136 505 136 HOH HOH . D 4 HOH A 137 506 137 HOH HOH . D 4 HOH A 138 507 138 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 16.335 9.226 34.481 1 78.98 ? PB ADP 368 A 1 HETATM 2 O O1B ADP . . . B 2 14.861 9.142 34.742 1 78.75 ? O1B ADP 368 A 1 HETATM 3 O O2B ADP . . . B 2 16.554 9.394 33 1 78.06 ? O2B ADP 368 A 1 HETATM 4 O O3B ADP . . . B 2 17.227 10.037 35.353 1 77.64 ? O3B ADP 368 A 1 HETATM 5 P PA ADP . . . B 2 18.168 7.199 34.016 1 73.03 ? PA ADP 368 A 1 HETATM 6 O O1A ADP . . . B 2 18.615 8.158 32.975 1 73.05 ? O1A ADP 368 A 1 HETATM 7 O O2A ADP . . . B 2 17.886 5.823 33.587 1 72.93 ? O2A ADP 368 A 1 HETATM 8 O O3A ADP . . . B 2 16.893 7.762 34.783 1 76.58 ? O3A ADP 368 A 1 HETATM 9 O O5' ADP . . . B 2 19.248 7.21 35.153 1 69.84 ? O5' ADP 368 A 1 HETATM 10 C C5' ADP . . . B 2 19.896 8.431 35.444 1 64.08 ? C5' ADP 368 A 1 HETATM 11 C C4' ADP . . . B 2 21.346 8.164 35.622 1 59.7 ? C4' ADP 368 A 1 HETATM 12 O O4' ADP . . . B 2 21.453 6.933 36.258 1 57.16 ? O4' ADP 368 A 1 HETATM 13 C C3' ADP . . . B 2 21.974 7.978 34.276 1 58.73 ? C3' ADP 368 A 1 HETATM 14 O O3' ADP . . . B 2 22.683 9.164 33.994 1 60.96 ? O3' ADP 368 A 1 HETATM 15 C C2' ADP . . . B 2 22.977 6.903 34.5 1 56.4 ? C2' ADP 368 A 1 HETATM 16 O O2' ADP . . . B 2 24.191 7.599 34.738 1 57.25 ? O2' ADP 368 A 1 HETATM 17 C C1' ADP . . . B 2 22.555 6.245 35.779 1 50.61 ? C1' ADP 368 A 1 HETATM 18 N N9 ADP . . . B 2 22.083 4.882 35.658 1 44.2 ? N9 ADP 368 A 1 HETATM 19 C C8 ADP . . . B 2 20.829 4.496 35.693 1 41.31 ? C8 ADP 368 A 1 HETATM 20 N N7 ADP . . . B 2 20.74 3.164 35.613 1 40.43 ? N7 ADP 368 A 1 HETATM 21 C C5 ADP . . . B 2 21.969 2.689 35.558 1 40.14 ? C5 ADP 368 A 1 HETATM 22 C C6 ADP . . . B 2 22.611 1.374 35.472 1 39.95 ? C6 ADP 368 A 1 HETATM 23 N N6 ADP . . . B 2 21.893 0.252 35.416 1 36.61 ? N6 ADP 368 A 1 HETATM 24 N N1 ADP . . . B 2 23.947 1.342 35.445 1 38 ? N1 ADP 368 A 1 HETATM 25 C C2 ADP . . . B 2 24.672 2.434 35.485 1 39.07 ? C2 ADP 368 A 1 HETATM 26 N N3 ADP . . . B 2 24.168 3.649 35.553 1 40.71 ? N3 ADP 368 A 1 HETATM 27 C C4 ADP . . . B 2 22.852 3.835 35.585 1 41.78 ? C4 ADP 368 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #