data_3QVF # _model_server_result.job_id gQvwotEdgvqyRoKbi4yqeQ _model_server_result.datetime_utc '2024-11-14 08:09:45' _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 3qvf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1260}' # _entry.id 3QVF # _exptl.entry_id 3QVF _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 120 _cell.entry_id 3QVF _cell.length_a 87.38 _cell.length_b 87.38 _cell.length_c 79 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QVF _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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 _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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 79 # _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 E O HOH . A HOH 330 1_555 D MG MG . A MG 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc2 E O HOH . A HOH 357 1_555 D MG MG . A MG 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc3 E O HOH . A HOH 375 1_555 D MG MG . A MG 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc4 B O1B ADP . A ADP 1260 1_555 D MG MG . A MG 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc5 B O2A ADP . A ADP 1260 1_555 D MG MG . A MG 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc6 C O3 FV1 . A FV1 4001 1_555 D MG MG . A MG 5000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? # _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 3QVF _atom_sites.fract_transf_matrix[1][1] 0.011444 _atom_sites.fract_transf_matrix[1][2] 0.006607 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013215 _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] 0.012658 _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 1260 1260 ADP ADP . C 3 FV1 A 1 4001 4001 FV1 FV1 . D 4 MG A 1 5000 5000 MG MG . E 5 HOH A 1 267 1 HOH HOH . E 5 HOH A 2 268 2 HOH HOH . E 5 HOH A 3 269 3 HOH HOH . E 5 HOH A 4 270 4 HOH HOH . E 5 HOH A 5 271 5 HOH HOH . E 5 HOH A 6 272 6 HOH HOH . E 5 HOH A 7 273 7 HOH HOH . E 5 HOH A 8 274 8 HOH HOH . E 5 HOH A 9 275 9 HOH HOH . E 5 HOH A 10 276 10 HOH HOH . E 5 HOH A 11 277 11 HOH HOH . E 5 HOH A 12 278 12 HOH HOH . E 5 HOH A 13 279 13 HOH HOH . E 5 HOH A 14 280 14 HOH HOH . E 5 HOH A 15 281 15 HOH HOH . E 5 HOH A 16 282 16 HOH HOH . E 5 HOH A 17 283 17 HOH HOH . E 5 HOH A 18 284 18 HOH HOH . E 5 HOH A 19 285 19 HOH HOH . E 5 HOH A 20 286 20 HOH HOH . E 5 HOH A 21 287 21 HOH HOH . E 5 HOH A 22 288 22 HOH HOH . E 5 HOH A 23 289 23 HOH HOH . E 5 HOH A 24 290 24 HOH HOH . E 5 HOH A 25 291 25 HOH HOH . E 5 HOH A 26 292 26 HOH HOH . E 5 HOH A 27 293 27 HOH HOH . E 5 HOH A 28 294 28 HOH HOH . E 5 HOH A 29 295 29 HOH HOH . E 5 HOH A 30 296 30 HOH HOH . E 5 HOH A 31 297 31 HOH HOH . E 5 HOH A 32 298 32 HOH HOH . E 5 HOH A 33 299 33 HOH HOH . E 5 HOH A 34 300 34 HOH HOH . E 5 HOH A 35 301 35 HOH HOH . E 5 HOH A 36 302 36 HOH HOH . E 5 HOH A 37 303 37 HOH HOH . E 5 HOH A 38 304 38 HOH HOH . E 5 HOH A 39 305 39 HOH HOH . E 5 HOH A 40 306 40 HOH HOH . E 5 HOH A 41 307 41 HOH HOH . E 5 HOH A 42 308 42 HOH HOH . E 5 HOH A 43 309 43 HOH HOH . E 5 HOH A 44 310 44 HOH HOH . E 5 HOH A 45 311 45 HOH HOH . E 5 HOH A 46 312 46 HOH HOH . E 5 HOH A 47 313 47 HOH HOH . E 5 HOH A 48 314 48 HOH HOH . E 5 HOH A 49 315 49 HOH HOH . E 5 HOH A 50 316 50 HOH HOH . E 5 HOH A 51 317 51 HOH HOH . E 5 HOH A 52 318 52 HOH HOH . E 5 HOH A 53 319 53 HOH HOH . E 5 HOH A 54 320 54 HOH HOH . E 5 HOH A 55 321 55 HOH HOH . E 5 HOH A 56 322 56 HOH HOH . E 5 HOH A 57 323 57 HOH HOH . E 5 HOH A 58 324 58 HOH HOH . E 5 HOH A 59 325 59 HOH HOH . E 5 HOH A 60 326 60 HOH HOH . E 5 HOH A 61 327 61 HOH HOH . E 5 HOH A 62 328 62 HOH HOH . E 5 HOH A 63 329 63 HOH HOH . E 5 HOH A 64 330 64 HOH HOH . E 5 HOH A 65 331 65 HOH HOH . E 5 HOH A 66 332 66 HOH HOH . E 5 HOH A 67 333 67 HOH HOH . E 5 HOH A 68 334 68 HOH HOH . E 5 HOH A 69 335 69 HOH HOH . E 5 HOH A 70 336 70 HOH HOH . E 5 HOH A 71 337 71 HOH HOH . E 5 HOH A 72 338 72 HOH HOH . E 5 HOH A 73 339 73 HOH HOH . E 5 HOH A 74 340 74 HOH HOH . E 5 HOH A 75 341 75 HOH HOH . E 5 HOH A 76 342 76 HOH HOH . E 5 HOH A 77 343 77 HOH HOH . E 5 HOH A 78 344 78 HOH HOH . E 5 HOH A 79 345 79 HOH HOH . E 5 HOH A 80 346 80 HOH HOH . E 5 HOH A 81 347 81 HOH HOH . E 5 HOH A 82 348 82 HOH HOH . E 5 HOH A 83 349 83 HOH HOH . E 5 HOH A 84 350 84 HOH HOH . E 5 HOH A 85 351 85 HOH HOH . E 5 HOH A 86 352 86 HOH HOH . E 5 HOH A 87 353 87 HOH HOH . E 5 HOH A 88 354 88 HOH HOH . E 5 HOH A 89 355 89 HOH HOH . E 5 HOH A 90 356 90 HOH HOH . E 5 HOH A 91 357 91 HOH HOH . E 5 HOH A 92 358 92 HOH HOH . E 5 HOH A 93 359 93 HOH HOH . E 5 HOH A 94 360 94 HOH HOH . E 5 HOH A 95 361 95 HOH HOH . E 5 HOH A 96 362 96 HOH HOH . E 5 HOH A 97 363 97 HOH HOH . E 5 HOH A 98 364 98 HOH HOH . E 5 HOH A 99 365 99 HOH HOH . E 5 HOH A 100 366 100 HOH HOH . E 5 HOH A 101 367 101 HOH HOH . E 5 HOH A 102 368 102 HOH HOH . E 5 HOH A 103 369 103 HOH HOH . E 5 HOH A 104 370 104 HOH HOH . E 5 HOH A 105 371 105 HOH HOH . E 5 HOH A 106 372 106 HOH HOH . E 5 HOH A 107 373 107 HOH HOH . E 5 HOH A 108 374 108 HOH HOH . E 5 HOH A 109 375 109 HOH HOH . E 5 HOH A 110 376 110 HOH HOH . E 5 HOH A 111 377 111 HOH HOH . E 5 HOH A 112 378 112 HOH HOH . E 5 HOH A 113 379 113 HOH HOH . E 5 HOH A 114 380 114 HOH HOH . E 5 HOH A 115 381 115 HOH HOH . E 5 HOH A 116 382 116 HOH HOH . E 5 HOH A 117 383 117 HOH HOH . E 5 HOH A 118 384 118 HOH HOH . E 5 HOH A 119 385 119 HOH HOH . E 5 HOH A 120 386 120 HOH HOH . E 5 HOH A 121 387 121 HOH HOH . E 5 HOH A 122 388 122 HOH HOH . E 5 HOH A 123 389 123 HOH HOH . E 5 HOH A 124 390 124 HOH HOH . E 5 HOH A 125 391 125 HOH HOH . E 5 HOH A 126 392 126 HOH HOH . E 5 HOH A 127 393 127 HOH HOH . E 5 HOH A 128 394 128 HOH HOH . E 5 HOH A 129 395 129 HOH HOH . E 5 HOH A 130 396 130 HOH HOH . E 5 HOH A 131 397 131 HOH HOH . E 5 HOH A 132 398 132 HOH HOH . E 5 HOH A 133 399 133 HOH HOH . E 5 HOH A 134 400 134 HOH HOH . E 5 HOH A 135 401 135 HOH HOH . E 5 HOH A 136 402 136 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 -6.959 30.206 35.531 1 44.86 ? PB ADP 1260 A 1 HETATM 2 O O1B ADP . . . B 2 -6.014 30.909 36.435 1 43.65 ? O1B ADP 1260 A 1 HETATM 3 O O2B ADP . . . B 2 -6.94 30.803 34.175 1 46.39 ? O2B ADP 1260 A 1 HETATM 4 O O3B ADP . . . B 2 -6.823 28.706 35.559 1 48.08 ? O3B ADP 1260 A 1 HETATM 5 P PA ADP . . . B 2 -9.114 31.105 37.388 1 44.79 ? PA ADP 1260 A 1 HETATM 6 O O1A ADP . . . B 2 -10.18 30.167 37.911 1 41.81 ? O1A ADP 1260 A 1 HETATM 7 O O2A ADP . . . B 2 -8.06 31.295 38.445 1 44.63 ? O2A ADP 1260 A 1 HETATM 8 O O3A ADP . . . B 2 -8.478 30.384 36.106 1 44.92 ? O3A ADP 1260 A 1 HETATM 9 O O5' ADP . . . B 2 -9.694 32.522 36.847 1 41.65 ? O5' ADP 1260 A 1 HETATM 10 C C5' ADP . . . B 2 -10.745 32.485 35.875 1 46.93 ? C5' ADP 1260 A 1 HETATM 11 C C4' ADP . . . B 2 -12.087 32.526 36.594 1 47.21 ? C4' ADP 1260 A 1 HETATM 12 O O4' ADP . . . B 2 -12.303 33.82 37.127 1 46.96 ? O4' ADP 1260 A 1 HETATM 13 C C3' ADP . . . B 2 -13.303 32.321 35.681 1 45.76 ? C3' ADP 1260 A 1 HETATM 14 O O3' ADP . . . B 2 -13.516 30.916 35.465 1 45.36 ? O3' ADP 1260 A 1 HETATM 15 C C2' ADP . . . B 2 -14.393 32.963 36.514 1 46.84 ? C2' ADP 1260 A 1 HETATM 16 O O2' ADP . . . B 2 -15.064 31.965 37.28 1 47.34 ? O2' ADP 1260 A 1 HETATM 17 C C1' ADP . . . B 2 -13.67 33.905 37.485 1 45.28 ? C1' ADP 1260 A 1 HETATM 18 N N9 ADP . . . B 2 -14.201 35.255 37.353 1 42.21 ? N9 ADP 1260 A 1 HETATM 19 C C8 ADP . . . B 2 -14.535 36.026 38.405 1 42.01 ? C8 ADP 1260 A 1 HETATM 20 N N7 ADP . . . B 2 -15.042 37.195 37.989 1 44.84 ? N7 ADP 1260 A 1 HETATM 21 C C5 ADP . . . B 2 -15.071 37.181 36.651 1 44.64 ? C5 ADP 1260 A 1 HETATM 22 C C6 ADP . . . B 2 -15.511 38.12 35.622 1 45.3 ? C6 ADP 1260 A 1 HETATM 23 N N6 ADP . . . B 2 -16.039 39.333 35.958 1 47.68 ? N6 ADP 1260 A 1 HETATM 24 N N1 ADP . . . B 2 -15.344 37.739 34.34 1 45.63 ? N1 ADP 1260 A 1 HETATM 25 C C2 ADP . . . B 2 -14.827 36.521 34.018 1 45.13 ? C2 ADP 1260 A 1 HETATM 26 N N3 ADP . . . B 2 -14.432 35.59 34.909 1 41.46 ? N3 ADP 1260 A 1 HETATM 27 C C4 ADP . . . B 2 -14.524 35.878 36.232 1 44.72 ? C4 ADP 1260 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #