data_3F61 # _model_server_result.job_id cigB52mpBAWarY4ryQrixg _model_server_result.datetime_utc '2024-12-14 01:14:18' _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 3f61 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":340}' # _entry.id 3F61 # _exptl.entry_id 3F61 _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 3F61 _cell.length_a 38.981 _cell.length_b 51.542 _cell.length_c 152.434 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3F61 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 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 OD1 ASN 146 A ASN 143 1_555 C MG MG . A MG 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc2 A OD2 ASP 159 A ASP 156 1_555 C MG MG . A MG 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc3 C MG MG . A MG 310 1_555 B O1B ADP . A ADP 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc4 C MG MG . A MG 310 1_555 B O2A ADP . A ADP 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc5 C MG MG . A MG 310 1_555 G O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc6 C MG MG . A MG 310 1_555 G O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? # _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 3F61 _atom_sites.fract_transf_matrix[1][1] 0.025654 _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] 0.019402 _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] 0.00656 _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 1 340 340 ADP ADP . C 3 MG A 1 310 2 MG MG . D 3 MG A 1 311 1 MG MG . E 3 MG A 1 312 1 MG MG . F 3 MG A 1 313 1 MG MG . G 4 HOH A 1 314 22 HOH HOH . G 4 HOH A 2 315 23 HOH HOH . G 4 HOH A 3 316 24 HOH HOH . G 4 HOH A 4 317 25 HOH HOH . G 4 HOH A 5 318 26 HOH HOH . G 4 HOH A 6 319 27 HOH HOH . G 4 HOH A 7 320 28 HOH HOH . G 4 HOH A 8 321 29 HOH HOH . G 4 HOH A 9 322 30 HOH HOH . G 4 HOH A 10 323 31 HOH HOH . G 4 HOH A 11 324 32 HOH HOH . G 4 HOH A 12 325 33 HOH HOH . G 4 HOH A 13 326 34 HOH HOH . G 4 HOH A 14 327 35 HOH HOH . G 4 HOH A 15 328 36 HOH HOH . G 4 HOH A 16 329 37 HOH HOH . G 4 HOH A 17 330 38 HOH HOH . G 4 HOH A 18 331 40 HOH HOH . G 4 HOH A 19 332 41 HOH HOH . G 4 HOH A 20 333 42 HOH HOH . G 4 HOH A 21 334 43 HOH HOH . G 4 HOH A 22 335 44 HOH HOH . G 4 HOH A 23 336 46 HOH HOH . G 4 HOH A 24 337 47 HOH HOH . G 4 HOH A 25 338 48 HOH HOH . G 4 HOH A 26 339 49 HOH HOH . G 4 HOH A 27 341 51 HOH HOH . G 4 HOH A 28 342 52 HOH HOH . G 4 HOH A 29 343 53 HOH HOH . G 4 HOH A 30 344 54 HOH HOH . G 4 HOH A 31 345 55 HOH HOH . G 4 HOH A 32 346 56 HOH HOH . G 4 HOH A 33 347 57 HOH HOH . G 4 HOH A 34 348 58 HOH HOH . G 4 HOH A 35 349 60 HOH HOH . G 4 HOH A 36 350 61 HOH HOH . G 4 HOH A 37 351 62 HOH HOH . G 4 HOH A 38 352 63 HOH HOH . G 4 HOH A 39 353 64 HOH HOH . G 4 HOH A 40 354 67 HOH HOH . G 4 HOH A 41 355 68 HOH HOH . G 4 HOH A 42 356 70 HOH HOH . G 4 HOH A 43 357 71 HOH HOH . G 4 HOH A 44 358 72 HOH HOH . G 4 HOH A 45 359 73 HOH HOH . G 4 HOH A 46 360 74 HOH HOH . G 4 HOH A 47 361 75 HOH HOH . G 4 HOH A 48 362 78 HOH HOH . G 4 HOH A 49 363 79 HOH HOH . G 4 HOH A 50 364 80 HOH HOH . G 4 HOH A 51 365 81 HOH HOH . G 4 HOH A 52 366 82 HOH HOH . G 4 HOH A 53 367 83 HOH HOH . G 4 HOH A 54 368 84 HOH HOH . G 4 HOH A 55 369 86 HOH HOH . G 4 HOH A 56 370 87 HOH HOH . G 4 HOH A 57 371 88 HOH HOH . G 4 HOH A 58 372 89 HOH HOH . G 4 HOH A 59 373 91 HOH HOH . G 4 HOH A 60 374 92 HOH HOH . G 4 HOH A 61 375 93 HOH HOH . G 4 HOH A 62 376 94 HOH HOH . G 4 HOH A 63 377 95 HOH HOH . G 4 HOH A 64 378 96 HOH HOH . G 4 HOH A 65 379 97 HOH HOH . G 4 HOH A 66 380 98 HOH HOH . G 4 HOH A 67 381 99 HOH HOH . G 4 HOH A 68 382 100 HOH HOH . G 4 HOH A 69 383 101 HOH HOH . G 4 HOH A 70 384 103 HOH HOH . G 4 HOH A 71 385 105 HOH HOH . G 4 HOH A 72 386 106 HOH HOH . G 4 HOH A 73 387 107 HOH HOH . G 4 HOH A 74 388 108 HOH HOH . G 4 HOH A 75 389 109 HOH HOH . G 4 HOH A 76 390 113 HOH HOH . G 4 HOH A 77 391 114 HOH HOH . G 4 HOH A 78 392 115 HOH HOH . G 4 HOH A 79 393 116 HOH HOH . G 4 HOH A 80 394 117 HOH HOH . G 4 HOH A 81 395 118 HOH HOH . G 4 HOH A 82 396 121 HOH HOH . G 4 HOH A 83 397 122 HOH HOH . G 4 HOH A 84 398 124 HOH HOH . G 4 HOH A 85 399 125 HOH HOH . G 4 HOH A 86 400 127 HOH HOH . G 4 HOH A 87 401 128 HOH HOH . G 4 HOH A 88 402 129 HOH HOH . G 4 HOH A 89 403 133 HOH HOH . G 4 HOH A 90 404 135 HOH HOH . G 4 HOH A 91 405 136 HOH HOH . G 4 HOH A 92 406 137 HOH HOH . G 4 HOH A 93 407 143 HOH HOH . G 4 HOH A 94 408 145 HOH HOH . G 4 HOH A 95 409 146 HOH HOH . G 4 HOH A 96 410 151 HOH HOH . G 4 HOH A 97 411 152 HOH HOH . G 4 HOH A 98 412 2 HOH HOH . G 4 HOH A 99 413 4 HOH HOH . G 4 HOH A 100 414 7 HOH HOH . G 4 HOH A 101 415 8 HOH HOH . G 4 HOH A 102 416 9 HOH HOH . G 4 HOH A 103 417 10 HOH HOH . G 4 HOH A 104 418 11 HOH HOH . G 4 HOH A 105 419 13 HOH HOH . G 4 HOH A 106 420 2 HOH HOH . G 4 HOH A 107 421 3 HOH HOH . G 4 HOH A 108 422 7 HOH HOH . G 4 HOH A 109 423 12 HOH HOH . G 4 HOH A 110 424 16 HOH HOH . G 4 HOH A 111 425 17 HOH HOH . G 4 HOH A 112 426 19 HOH HOH . G 4 HOH A 113 427 20 HOH HOH . G 4 HOH A 114 428 22 HOH HOH . G 4 HOH A 115 429 16 HOH HOH . G 4 HOH A 116 430 2 HOH HOH . G 4 HOH A 117 431 4 HOH HOH . G 4 HOH A 118 432 7 HOH HOH . G 4 HOH A 119 433 8 HOH HOH . G 4 HOH A 120 434 10 HOH HOH . G 4 HOH A 121 435 12 HOH HOH . G 4 HOH A 122 436 13 HOH HOH . G 4 HOH A 123 437 14 HOH HOH . G 4 HOH A 124 438 15 HOH HOH . G 4 HOH A 125 439 17 HOH HOH . G 4 HOH A 126 440 18 HOH HOH . G 4 HOH A 127 441 19 HOH HOH . G 4 HOH A 128 442 20 HOH HOH . G 4 HOH A 129 443 1 HOH HOH . G 4 HOH A 130 444 2 HOH HOH . G 4 HOH A 131 445 3 HOH HOH . G 4 HOH A 132 446 4 HOH HOH . G 4 HOH A 133 447 5 HOH HOH . G 4 HOH A 134 448 6 HOH HOH . G 4 HOH A 135 449 7 HOH HOH . G 4 HOH A 136 450 8 HOH HOH . G 4 HOH A 137 451 9 HOH HOH . G 4 HOH A 138 452 10 HOH HOH . G 4 HOH A 139 453 11 HOH HOH . G 4 HOH A 140 454 12 HOH HOH . G 4 HOH A 141 455 13 HOH HOH . G 4 HOH A 142 456 14 HOH HOH . G 4 HOH A 143 457 15 HOH HOH . G 4 HOH A 144 458 16 HOH HOH . G 4 HOH A 145 459 17 HOH HOH . G 4 HOH A 146 460 18 HOH HOH . G 4 HOH A 147 461 20 HOH HOH . G 4 HOH A 148 462 21 HOH HOH . G 4 HOH A 149 463 22 HOH HOH . G 4 HOH A 150 464 23 HOH HOH . G 4 HOH A 151 465 24 HOH HOH . G 4 HOH A 152 466 25 HOH HOH . G 4 HOH A 153 467 26 HOH HOH . G 4 HOH A 154 468 27 HOH HOH . G 4 HOH A 155 469 28 HOH HOH . G 4 HOH A 156 470 29 HOH HOH . G 4 HOH A 157 471 1 HOH HOH . G 4 HOH A 158 472 2 HOH HOH . G 4 HOH A 159 473 3 HOH HOH . G 4 HOH A 160 474 4 HOH HOH . G 4 HOH A 161 475 5 HOH HOH . G 4 HOH A 162 476 1 HOH HOH . G 4 HOH A 163 477 2 HOH HOH . G 4 HOH A 164 478 1 HOH HOH . G 4 HOH A 165 479 1 HOH HOH . G 4 HOH A 166 480 2 HOH HOH . G 4 HOH A 167 481 3 HOH HOH . G 4 HOH A 168 482 4 HOH HOH . G 4 HOH A 169 483 5 HOH HOH . G 4 HOH A 170 484 6 HOH HOH . G 4 HOH A 171 485 7 HOH HOH . G 4 HOH A 172 486 8 HOH HOH . G 4 HOH A 173 487 9 HOH HOH . G 4 HOH A 174 488 11 HOH HOH . G 4 HOH A 175 489 12 HOH HOH . G 4 HOH A 176 490 13 HOH HOH . G 4 HOH A 177 491 14 HOH HOH . G 4 HOH A 178 492 15 HOH HOH . G 4 HOH A 179 493 16 HOH HOH . G 4 HOH A 180 494 17 HOH HOH . G 4 HOH A 181 495 18 HOH HOH . G 4 HOH A 182 496 19 HOH HOH . G 4 HOH A 183 497 20 HOH HOH . G 4 HOH A 184 498 21 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 -10.994 10.754 -11.467 1 27.35 ? PB ADP 340 A 1 HETATM 2 O O1B ADP . . . B 2 -10.871 11.285 -12.88 1 25.91 ? O1B ADP 340 A 1 HETATM 3 O O2B ADP . . . B 2 -12.276 10.096 -11.089 1 29.93 ? O2B ADP 340 A 1 HETATM 4 O O3B ADP . . . B 2 -9.797 9.868 -11.151 1 28.56 ? O3B ADP 340 A 1 HETATM 5 P PA ADP . . . B 2 -9.998 13.326 -10.57 1 20.96 ? PA ADP 340 A 1 HETATM 6 O O1A ADP . . . B 2 -9.458 13.718 -9.231 1 22.63 ? O1A ADP 340 A 1 HETATM 7 O O2A ADP . . . B 2 -9.038 13.29 -11.739 1 20.37 ? O2A ADP 340 A 1 HETATM 8 O O3A ADP . . . B 2 -10.882 11.987 -10.424 1 21.06 ? O3A ADP 340 A 1 HETATM 9 O O5' ADP . . . B 2 -11.117 14.392 -10.946 1 19.72 ? O5' ADP 340 A 1 HETATM 10 C C5' ADP . . . B 2 -12.272 14.426 -10.103 1 19.1 ? C5' ADP 340 A 1 HETATM 11 C C4' ADP . . . B 2 -13.434 15.116 -10.809 1 19.81 ? C4' ADP 340 A 1 HETATM 12 O O4' ADP . . . B 2 -13.132 16.498 -10.913 1 19.14 ? O4' ADP 340 A 1 HETATM 13 C C3' ADP . . . B 2 -13.593 14.708 -12.254 1 18.96 ? C3' ADP 340 A 1 HETATM 14 O O3' ADP . . . B 2 -14.372 13.526 -12.435 1 20.88 ? O3' ADP 340 A 1 HETATM 15 C C2' ADP . . . B 2 -14.309 15.884 -12.848 1 21.42 ? C2' ADP 340 A 1 HETATM 16 O O2' ADP . . . B 2 -15.682 15.873 -12.407 1 23.54 ? O2' ADP 340 A 1 HETATM 17 C C1' ADP . . . B 2 -13.681 17.046 -12.117 1 18.63 ? C1' ADP 340 A 1 HETATM 18 N N9 ADP . . . B 2 -12.55 17.611 -12.894 1 16.14 ? N9 ADP 340 A 1 HETATM 19 C C8 ADP . . . B 2 -11.313 17.07 -12.989 1 16.63 ? C8 ADP 340 A 1 HETATM 20 N N7 ADP . . . B 2 -10.52 17.877 -13.742 1 18.3 ? N7 ADP 340 A 1 HETATM 21 C C5 ADP . . . B 2 -11.253 18.943 -14.146 1 16.68 ? C5 ADP 340 A 1 HETATM 22 C C6 ADP . . . B 2 -10.988 20.138 -14.986 1 19.02 ? C6 ADP 340 A 1 HETATM 23 N N6 ADP . . . B 2 -9.762 20.354 -15.512 1 20.14 ? N6 ADP 340 A 1 HETATM 24 N N1 ADP . . . B 2 -12.01 20.995 -15.166 1 18.72 ? N1 ADP 340 A 1 HETATM 25 C C2 ADP . . . B 2 -13.223 20.78 -14.593 1 17.83 ? C2 ADP 340 A 1 HETATM 26 N N3 ADP . . . B 2 -13.546 19.694 -13.833 1 18.91 ? N3 ADP 340 A 1 HETATM 27 C C4 ADP . . . B 2 -12.59 18.764 -13.579 1 17.3 ? C4 ADP 340 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #