data_3EH9 # _model_server_result.job_id XjUcFbolr806bUbNcmsALA _model_server_result.datetime_utc '2025-02-18 00:42:43' _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 3eh9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3EH9 # _exptl.entry_id 3EH9 _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 3EH9 _cell.length_a 46.862 _cell.length_b 62.675 _cell.length_c 88.23 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EH9 _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 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 # _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 # _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 3EH9 _atom_sites.fract_transf_matrix[1][1] 0.021339 _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] 0.015955 _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] 0.011334 _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 1 1 ADP ADP . C 3 SO4 A 1 296 1 SO4 SO4 . D 3 SO4 A 1 297 2 SO4 SO4 . E 4 HOH A 1 298 2 HOH HOH . E 4 HOH A 2 299 3 HOH HOH . E 4 HOH A 3 300 4 HOH HOH . E 4 HOH A 4 301 5 HOH HOH . E 4 HOH A 5 302 6 HOH HOH . E 4 HOH A 6 303 7 HOH HOH . E 4 HOH A 7 304 8 HOH HOH . E 4 HOH A 8 305 9 HOH HOH . E 4 HOH A 9 306 10 HOH HOH . E 4 HOH A 10 307 11 HOH HOH . E 4 HOH A 11 308 12 HOH HOH . E 4 HOH A 12 309 13 HOH HOH . E 4 HOH A 13 310 14 HOH HOH . E 4 HOH A 14 311 15 HOH HOH . E 4 HOH A 15 312 16 HOH HOH . E 4 HOH A 16 313 17 HOH HOH . E 4 HOH A 17 314 18 HOH HOH . E 4 HOH A 18 315 19 HOH HOH . E 4 HOH A 19 316 20 HOH HOH . E 4 HOH A 20 317 21 HOH HOH . E 4 HOH A 21 318 22 HOH HOH . E 4 HOH A 22 319 23 HOH HOH . E 4 HOH A 23 320 24 HOH HOH . E 4 HOH A 24 321 25 HOH HOH . E 4 HOH A 25 322 26 HOH HOH . E 4 HOH A 26 323 27 HOH HOH . E 4 HOH A 27 324 28 HOH HOH . E 4 HOH A 28 325 29 HOH HOH . E 4 HOH A 29 326 30 HOH HOH . E 4 HOH A 30 327 31 HOH HOH . E 4 HOH A 31 328 32 HOH HOH . E 4 HOH A 32 329 33 HOH HOH . E 4 HOH A 33 330 34 HOH HOH . E 4 HOH A 34 331 35 HOH HOH . E 4 HOH A 35 332 36 HOH HOH . E 4 HOH A 36 333 37 HOH HOH . E 4 HOH A 37 334 38 HOH HOH . E 4 HOH A 38 335 39 HOH HOH . E 4 HOH A 39 336 40 HOH HOH . E 4 HOH A 40 337 41 HOH HOH . E 4 HOH A 41 338 42 HOH HOH . E 4 HOH A 42 339 43 HOH HOH . E 4 HOH A 43 340 44 HOH HOH . E 4 HOH A 44 341 45 HOH HOH . E 4 HOH A 45 342 46 HOH HOH . E 4 HOH A 46 343 47 HOH HOH . E 4 HOH A 47 344 48 HOH HOH . E 4 HOH A 48 345 49 HOH HOH . E 4 HOH A 49 346 50 HOH HOH . E 4 HOH A 50 347 51 HOH HOH . E 4 HOH A 51 348 52 HOH HOH . E 4 HOH A 52 349 53 HOH HOH . E 4 HOH A 53 350 54 HOH HOH . E 4 HOH A 54 351 55 HOH HOH . E 4 HOH A 55 352 56 HOH HOH . E 4 HOH A 56 353 57 HOH HOH . E 4 HOH A 57 354 58 HOH HOH . E 4 HOH A 58 355 59 HOH HOH . E 4 HOH A 59 356 60 HOH HOH . E 4 HOH A 60 357 61 HOH HOH . E 4 HOH A 61 358 62 HOH HOH . E 4 HOH A 62 359 63 HOH HOH . E 4 HOH A 63 360 64 HOH HOH . E 4 HOH A 64 361 65 HOH HOH . E 4 HOH A 65 362 66 HOH HOH . E 4 HOH A 66 363 67 HOH HOH . E 4 HOH A 67 364 68 HOH HOH . E 4 HOH A 68 365 69 HOH HOH . E 4 HOH A 69 366 70 HOH HOH . E 4 HOH A 70 367 71 HOH HOH . E 4 HOH A 71 368 72 HOH HOH . E 4 HOH A 72 369 73 HOH HOH . E 4 HOH A 73 370 74 HOH HOH . E 4 HOH A 74 371 75 HOH HOH . E 4 HOH A 75 372 76 HOH HOH . E 4 HOH A 76 373 77 HOH HOH . E 4 HOH A 77 374 78 HOH HOH . E 4 HOH A 78 375 79 HOH HOH . E 4 HOH A 79 376 80 HOH HOH . E 4 HOH A 80 377 81 HOH HOH . E 4 HOH A 81 378 82 HOH HOH . E 4 HOH A 82 379 83 HOH HOH . E 4 HOH A 83 380 84 HOH HOH . E 4 HOH A 84 381 85 HOH HOH . E 4 HOH A 85 382 86 HOH HOH . E 4 HOH A 86 383 87 HOH HOH . E 4 HOH A 87 384 88 HOH HOH . E 4 HOH A 88 385 89 HOH HOH . E 4 HOH A 89 386 90 HOH HOH . E 4 HOH A 90 387 91 HOH HOH . E 4 HOH A 91 388 92 HOH HOH . E 4 HOH A 92 389 93 HOH HOH . E 4 HOH A 93 390 94 HOH HOH . E 4 HOH A 94 391 95 HOH HOH . E 4 HOH A 95 392 96 HOH HOH . E 4 HOH A 96 393 97 HOH HOH . E 4 HOH A 97 394 98 HOH HOH . E 4 HOH A 98 395 99 HOH HOH . E 4 HOH A 99 396 100 HOH HOH . E 4 HOH A 100 397 101 HOH HOH . E 4 HOH A 101 398 102 HOH HOH . E 4 HOH A 102 399 103 HOH HOH . E 4 HOH A 103 400 104 HOH HOH . E 4 HOH A 104 401 105 HOH HOH . E 4 HOH A 105 402 106 HOH HOH . E 4 HOH A 106 403 107 HOH HOH . E 4 HOH A 107 404 108 HOH HOH . E 4 HOH A 108 405 109 HOH HOH . E 4 HOH A 109 406 110 HOH HOH . E 4 HOH A 110 407 111 HOH HOH . E 4 HOH A 111 408 112 HOH HOH . E 4 HOH A 112 409 113 HOH HOH . E 4 HOH A 113 410 114 HOH HOH . E 4 HOH A 114 411 115 HOH HOH . E 4 HOH A 115 412 116 HOH HOH . E 4 HOH A 116 413 117 HOH HOH . E 4 HOH A 117 414 118 HOH HOH . E 4 HOH A 118 415 119 HOH HOH . E 4 HOH A 119 416 120 HOH HOH . E 4 HOH A 120 417 121 HOH HOH . E 4 HOH A 121 418 122 HOH HOH . E 4 HOH A 122 419 123 HOH HOH . E 4 HOH A 123 420 124 HOH HOH . E 4 HOH A 124 421 125 HOH HOH . E 4 HOH A 125 422 126 HOH HOH . E 4 HOH A 126 423 127 HOH HOH . E 4 HOH A 127 424 128 HOH HOH . E 4 HOH A 128 425 129 HOH HOH . E 4 HOH A 129 426 130 HOH HOH . E 4 HOH A 130 427 131 HOH HOH . E 4 HOH A 131 428 132 HOH HOH . E 4 HOH A 132 429 133 HOH HOH . E 4 HOH A 133 430 134 HOH HOH . E 4 HOH A 134 431 135 HOH HOH . E 4 HOH A 135 432 136 HOH HOH . E 4 HOH A 136 433 137 HOH HOH . E 4 HOH A 137 434 138 HOH HOH . E 4 HOH A 138 435 139 HOH HOH . E 4 HOH A 139 436 140 HOH HOH . E 4 HOH A 140 437 141 HOH HOH . E 4 HOH A 141 438 142 HOH HOH . E 4 HOH A 142 439 143 HOH HOH . E 4 HOH A 143 440 145 HOH HOH . E 4 HOH A 144 441 146 HOH HOH . E 4 HOH A 145 442 147 HOH HOH . E 4 HOH A 146 443 148 HOH HOH . E 4 HOH A 147 444 149 HOH HOH . E 4 HOH A 148 445 150 HOH HOH . E 4 HOH A 149 446 151 HOH HOH . E 4 HOH A 150 447 152 HOH HOH . E 4 HOH A 151 448 153 HOH HOH . E 4 HOH A 152 449 154 HOH HOH . E 4 HOH A 153 450 155 HOH HOH . E 4 HOH A 154 451 157 HOH HOH . E 4 HOH A 155 452 158 HOH HOH . E 4 HOH A 156 453 160 HOH HOH . E 4 HOH A 157 454 161 HOH HOH . E 4 HOH A 158 455 162 HOH HOH . E 4 HOH A 159 456 163 HOH HOH . E 4 HOH A 160 457 164 HOH HOH . E 4 HOH A 161 458 165 HOH HOH . E 4 HOH A 162 459 166 HOH HOH . E 4 HOH A 163 460 167 HOH HOH . E 4 HOH A 164 461 168 HOH HOH . E 4 HOH A 165 462 169 HOH HOH . E 4 HOH A 166 463 170 HOH HOH . E 4 HOH A 167 464 171 HOH HOH . E 4 HOH A 168 465 172 HOH HOH . E 4 HOH A 169 466 173 HOH HOH . E 4 HOH A 170 467 174 HOH HOH . E 4 HOH A 171 468 176 HOH HOH . E 4 HOH A 172 469 177 HOH HOH . E 4 HOH A 173 470 178 HOH HOH . E 4 HOH A 174 471 179 HOH HOH . E 4 HOH A 175 472 180 HOH HOH . E 4 HOH A 176 473 181 HOH HOH . E 4 HOH A 177 474 182 HOH HOH . E 4 HOH A 178 475 183 HOH HOH . E 4 HOH A 179 476 184 HOH HOH . E 4 HOH A 180 477 185 HOH HOH . E 4 HOH A 181 478 186 HOH HOH . E 4 HOH A 182 479 187 HOH HOH . E 4 HOH A 183 480 188 HOH HOH . E 4 HOH A 184 481 189 HOH HOH . E 4 HOH A 185 482 190 HOH HOH . E 4 HOH A 186 483 191 HOH HOH . E 4 HOH A 187 484 192 HOH HOH . E 4 HOH A 188 485 193 HOH HOH . E 4 HOH A 189 486 197 HOH HOH . E 4 HOH A 190 487 198 HOH HOH . E 4 HOH A 191 488 199 HOH HOH . E 4 HOH A 192 489 200 HOH HOH . E 4 HOH A 193 490 201 HOH HOH . E 4 HOH A 194 491 202 HOH HOH . E 4 HOH A 195 492 203 HOH HOH . E 4 HOH A 196 493 204 HOH HOH . E 4 HOH A 197 494 205 HOH HOH . E 4 HOH A 198 495 206 HOH HOH . E 4 HOH A 199 496 207 HOH HOH . E 4 HOH A 200 497 208 HOH HOH . E 4 HOH A 201 498 209 HOH HOH . E 4 HOH A 202 499 210 HOH HOH . E 4 HOH A 203 500 211 HOH HOH . E 4 HOH A 204 501 212 HOH HOH . E 4 HOH A 205 502 213 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 . A . B 2 -18.483 -2.061 -10.877 0.65 36.46 ? PB ADP 1 A 1 HETATM 2 P PB ADP . B . B 2 -18.67 1.257 -13.994 0.35 24.63 ? PB ADP 1 A 1 HETATM 3 O O1B ADP . A . B 2 -17.591 -1.442 -11.921 0.65 35.76 ? O1B ADP 1 A 1 HETATM 4 O O1B ADP . B . B 2 -19.217 -0.131 -14.245 0.35 27.11 ? O1B ADP 1 A 1 HETATM 5 O O2B ADP . A . B 2 -19.207 -3.294 -11.358 0.65 35.63 ? O2B ADP 1 A 1 HETATM 6 O O2B ADP . B . B 2 -17.178 1.279 -13.949 0.35 25.9 ? O2B ADP 1 A 1 HETATM 7 O O3B ADP . A . B 2 -17.797 -2.291 -9.567 0.65 35.55 ? O3B ADP 1 A 1 HETATM 8 O O3B ADP . B . B 2 -19.249 2.332 -14.881 0.35 24.64 ? O3B ADP 1 A 1 HETATM 9 P PA ADP . A . B 2 -19.929 0.471 -11.068 0.65 24.84 ? PA ADP 1 A 1 HETATM 10 P PA ADP . B . B 2 -19.917 0.834 -11.337 0.35 24.46 ? PA ADP 1 A 1 HETATM 11 O O1A ADP . A . B 2 -18.919 0.695 -12.178 0.65 27.09 ? O1A ADP 1 A 1 HETATM 12 O O1A ADP . B . B 2 -19.921 1.663 -10.072 0.35 23.71 ? O1A ADP 1 A 1 HETATM 13 O O2A ADP . A . B 2 -19.906 1.388 -9.863 0.65 23.34 ? O2A ADP 1 A 1 HETATM 14 O O2A ADP . B . B 2 -19.331 -0.557 -11.283 0.35 26.73 ? O2A ADP 1 A 1 HETATM 15 O O3A ADP . A . B 2 -19.756 -1.067 -10.567 0.65 29.81 ? O3A ADP 1 A 1 HETATM 16 O O3A ADP . B . B 2 -19.23 1.715 -12.527 0.35 25.51 ? O3A ADP 1 A 1 HETATM 17 O O5' ADP . A . B 2 -21.38 0.638 -11.741 0.65 26.38 ? O5' ADP 1 A 1 HETATM 18 O O5' ADP . B . B 2 -21.439 0.735 -11.809 0.35 25.38 ? O5' ADP 1 A 1 HETATM 19 C C5' ADP . . . B 2 -21.811 -0.144 -12.865 1 25.01 ? C5' ADP 1 A 1 HETATM 20 C C4' ADP . . . B 2 -22.805 0.589 -13.736 1 26.14 ? C4' ADP 1 A 1 HETATM 21 O O4' ADP . . . B 2 -24.03 0.795 -13 1 24.8 ? O4' ADP 1 A 1 HETATM 22 C C3' ADP . . . B 2 -22.362 1.982 -14.168 1 26.77 ? C3' ADP 1 A 1 HETATM 23 O O3' ADP . . . B 2 -21.499 1.958 -15.318 1 27.53 ? O3' ADP 1 A 1 HETATM 24 C C2' ADP . . . B 2 -23.682 2.691 -14.392 1 26.37 ? C2' ADP 1 A 1 HETATM 25 O O2' ADP . . . B 2 -24.305 2.329 -15.642 1 29.85 ? O2' ADP 1 A 1 HETATM 26 C C1' ADP . . . B 2 -24.548 2.109 -13.272 1 23.01 ? C1' ADP 1 A 1 HETATM 27 N N9 ADP . . . B 2 -24.46 2.96 -12.042 1 21.41 ? N9 ADP 1 A 1 HETATM 28 C C8 ADP . . . B 2 -23.519 2.921 -11.092 1 20.08 ? C8 ADP 1 A 1 HETATM 29 N N7 ADP . . . B 2 -23.763 3.821 -10.093 1 19.53 ? N7 ADP 1 A 1 HETATM 30 C C5 ADP . . . B 2 -24.901 4.417 -10.411 1 20.22 ? C5 ADP 1 A 1 HETATM 31 C C6 ADP . . . B 2 -25.736 5.446 -9.792 1 20.44 ? C6 ADP 1 A 1 HETATM 32 N N6 ADP . . . B 2 -25.314 6 -8.629 1 21.25 ? N6 ADP 1 A 1 HETATM 33 N N1 ADP . . . B 2 -26.852 5.829 -10.434 1 21.76 ? N1 ADP 1 A 1 HETATM 34 C C2 ADP . . . B 2 -27.251 5.273 -11.594 1 21.86 ? C2 ADP 1 A 1 HETATM 35 N N3 ADP . . . B 2 -26.517 4.323 -12.215 1 21.44 ? N3 ADP 1 A 1 HETATM 36 C C4 ADP . . . B 2 -25.373 3.855 -11.681 1 20.76 ? C4 ADP 1 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 376 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #