data_3U67 # _model_server_result.job_id jQNvS117zz0ihezn5Rb0rA _model_server_result.datetime_utc '2024-11-22 18:43:01' _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 3u67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":214}' # _entry.id 3U67 # _exptl.entry_id 3U67 _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 3U67 _cell.length_a 121.865 _cell.length_b 42.991 _cell.length_c 51.253 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U67 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 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' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 42.991 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 54 A ASN 36 1_555 C MG MG . A MG 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc2 B O1A ADP . A ADP 214 1_555 C MG MG . A MG 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc3 B O1B ADP . A ADP 214 1_555 C MG MG . A MG 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc4 C MG MG . A MG 215 1_555 G O HOH . A HOH 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 C MG MG . A MG 215 1_555 G O HOH . A HOH 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc6 C MG MG . A MG 215 1_555 G O HOH . A HOH 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? # _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 3U67 _atom_sites.fract_transf_matrix[1][1] 0.008206 _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] 0.023261 _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] 0.019511 _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 1 214 1 ADP ADP . C 3 MG A 1 215 1 MG MG . D 4 EDO A 1 216 1 EDO EDO . E 4 EDO A 1 217 1 EDO EDO . F 4 EDO A 1 218 1 EDO EDO . G 5 HOH A 1 219 1 HOH HOH . G 5 HOH A 2 220 2 HOH HOH . G 5 HOH A 3 221 3 HOH HOH . G 5 HOH A 4 222 4 HOH HOH . G 5 HOH A 5 223 5 HOH HOH . G 5 HOH A 6 224 6 HOH HOH . G 5 HOH A 7 225 7 HOH HOH . G 5 HOH A 8 226 8 HOH HOH . G 5 HOH A 9 227 9 HOH HOH . G 5 HOH A 10 228 10 HOH HOH . G 5 HOH A 11 229 11 HOH HOH . G 5 HOH A 12 230 12 HOH HOH . G 5 HOH A 13 231 13 HOH HOH . G 5 HOH A 14 232 14 HOH HOH . G 5 HOH A 15 233 15 HOH HOH . G 5 HOH A 16 234 16 HOH HOH . G 5 HOH A 17 235 17 HOH HOH . G 5 HOH A 18 236 18 HOH HOH . G 5 HOH A 19 237 19 HOH HOH . G 5 HOH A 20 238 20 HOH HOH . G 5 HOH A 21 239 21 HOH HOH . G 5 HOH A 22 240 22 HOH HOH . G 5 HOH A 23 241 23 HOH HOH . G 5 HOH A 24 242 24 HOH HOH . G 5 HOH A 25 243 25 HOH HOH . G 5 HOH A 26 244 26 HOH HOH . G 5 HOH A 27 245 27 HOH HOH . G 5 HOH A 28 246 28 HOH HOH . G 5 HOH A 29 247 29 HOH HOH . G 5 HOH A 30 248 30 HOH HOH . G 5 HOH A 31 249 31 HOH HOH . G 5 HOH A 32 250 32 HOH HOH . G 5 HOH A 33 251 33 HOH HOH . G 5 HOH A 34 252 34 HOH HOH . G 5 HOH A 35 253 35 HOH HOH . G 5 HOH A 36 254 36 HOH HOH . G 5 HOH A 37 255 37 HOH HOH . G 5 HOH A 38 256 38 HOH HOH . G 5 HOH A 39 257 39 HOH HOH . G 5 HOH A 40 258 40 HOH HOH . G 5 HOH A 41 259 41 HOH HOH . G 5 HOH A 42 260 42 HOH HOH . G 5 HOH A 43 261 43 HOH HOH . G 5 HOH A 44 262 44 HOH HOH . G 5 HOH A 45 263 45 HOH HOH . G 5 HOH A 46 264 46 HOH HOH . G 5 HOH A 47 265 47 HOH HOH . G 5 HOH A 48 266 48 HOH HOH . G 5 HOH A 49 267 49 HOH HOH . G 5 HOH A 50 268 50 HOH HOH . G 5 HOH A 51 269 51 HOH HOH . G 5 HOH A 52 270 52 HOH HOH . G 5 HOH A 53 271 53 HOH HOH . G 5 HOH A 54 272 54 HOH HOH . G 5 HOH A 55 273 55 HOH HOH . G 5 HOH A 56 274 56 HOH HOH . G 5 HOH A 57 275 57 HOH HOH . G 5 HOH A 58 276 58 HOH HOH . G 5 HOH A 59 277 59 HOH HOH . G 5 HOH A 60 278 60 HOH HOH . G 5 HOH A 61 279 61 HOH HOH . G 5 HOH A 62 280 62 HOH HOH . G 5 HOH A 63 281 63 HOH HOH . G 5 HOH A 64 282 64 HOH HOH . G 5 HOH A 65 283 65 HOH HOH . G 5 HOH A 66 284 66 HOH HOH . G 5 HOH A 67 285 67 HOH HOH . G 5 HOH A 68 286 68 HOH HOH . G 5 HOH A 69 287 69 HOH HOH . G 5 HOH A 70 288 70 HOH HOH . G 5 HOH A 71 289 71 HOH HOH . G 5 HOH A 72 290 72 HOH HOH . G 5 HOH A 73 291 73 HOH HOH . G 5 HOH A 74 292 74 HOH HOH . G 5 HOH A 75 293 75 HOH HOH . G 5 HOH A 76 294 76 HOH HOH . G 5 HOH A 77 295 77 HOH HOH . G 5 HOH A 78 296 78 HOH HOH . G 5 HOH A 79 297 79 HOH HOH . G 5 HOH A 80 298 80 HOH HOH . G 5 HOH A 81 299 81 HOH HOH . G 5 HOH A 82 300 82 HOH HOH . G 5 HOH A 83 301 83 HOH HOH . G 5 HOH A 84 302 84 HOH HOH . G 5 HOH A 85 303 85 HOH HOH . G 5 HOH A 86 304 86 HOH HOH . G 5 HOH A 87 305 87 HOH HOH . G 5 HOH A 88 306 88 HOH HOH . G 5 HOH A 89 307 89 HOH HOH . G 5 HOH A 90 308 90 HOH HOH . G 5 HOH A 91 309 91 HOH HOH . G 5 HOH A 92 310 92 HOH HOH . G 5 HOH A 93 311 93 HOH HOH . G 5 HOH A 94 312 94 HOH HOH . G 5 HOH A 95 313 95 HOH HOH . G 5 HOH A 96 314 96 HOH HOH . G 5 HOH A 97 315 97 HOH HOH . G 5 HOH A 98 316 98 HOH HOH . G 5 HOH A 99 317 99 HOH HOH . G 5 HOH A 100 318 100 HOH HOH . G 5 HOH A 101 319 101 HOH HOH . G 5 HOH A 102 320 102 HOH HOH . G 5 HOH A 103 321 103 HOH HOH . G 5 HOH A 104 322 104 HOH HOH . G 5 HOH A 105 323 105 HOH HOH . G 5 HOH A 106 324 106 HOH HOH . G 5 HOH A 107 325 107 HOH HOH . G 5 HOH A 108 326 108 HOH HOH . G 5 HOH A 109 327 109 HOH HOH . G 5 HOH A 110 328 110 HOH HOH . G 5 HOH A 111 329 111 HOH HOH . G 5 HOH A 112 330 112 HOH HOH . G 5 HOH A 113 331 113 HOH HOH . G 5 HOH A 114 332 114 HOH HOH . G 5 HOH A 115 333 115 HOH HOH . G 5 HOH A 116 334 116 HOH HOH . G 5 HOH A 117 335 117 HOH HOH . G 5 HOH A 118 336 118 HOH HOH . G 5 HOH A 119 337 119 HOH HOH . G 5 HOH A 120 338 120 HOH HOH . G 5 HOH A 121 339 121 HOH HOH . G 5 HOH A 122 340 122 HOH HOH . G 5 HOH A 123 341 123 HOH HOH . G 5 HOH A 124 342 124 HOH HOH . G 5 HOH A 125 343 125 HOH HOH . G 5 HOH A 126 344 126 HOH HOH . G 5 HOH A 127 345 127 HOH HOH . G 5 HOH A 128 346 128 HOH HOH . G 5 HOH A 129 347 129 HOH HOH . G 5 HOH A 130 348 130 HOH HOH . G 5 HOH A 131 349 131 HOH HOH . G 5 HOH A 132 350 132 HOH HOH . G 5 HOH A 133 351 133 HOH HOH . G 5 HOH A 134 352 134 HOH HOH . G 5 HOH A 135 353 135 HOH HOH . G 5 HOH A 136 354 136 HOH HOH . G 5 HOH A 137 355 137 HOH HOH . G 5 HOH A 138 356 138 HOH HOH . G 5 HOH A 139 357 139 HOH HOH . G 5 HOH A 140 358 140 HOH HOH . G 5 HOH A 141 359 141 HOH HOH . G 5 HOH A 142 360 142 HOH HOH . G 5 HOH A 143 361 143 HOH HOH . G 5 HOH A 144 362 144 HOH HOH . G 5 HOH A 145 363 145 HOH HOH . G 5 HOH A 146 364 146 HOH HOH . G 5 HOH A 147 365 147 HOH HOH . G 5 HOH A 148 366 148 HOH HOH . G 5 HOH A 149 367 149 HOH HOH . G 5 HOH A 150 368 150 HOH HOH . G 5 HOH A 151 369 151 HOH HOH . G 5 HOH A 152 370 152 HOH HOH . G 5 HOH A 153 371 153 HOH HOH . G 5 HOH A 154 372 154 HOH HOH . G 5 HOH A 155 373 155 HOH HOH . G 5 HOH A 156 374 156 HOH HOH . G 5 HOH A 157 375 157 HOH HOH . G 5 HOH A 158 376 158 HOH HOH . G 5 HOH A 159 377 159 HOH HOH . G 5 HOH A 160 378 160 HOH HOH . G 5 HOH A 161 379 161 HOH HOH . G 5 HOH A 162 380 162 HOH HOH . G 5 HOH A 163 381 163 HOH HOH . G 5 HOH A 164 382 164 HOH HOH . G 5 HOH A 165 383 165 HOH HOH . G 5 HOH A 166 384 166 HOH HOH . G 5 HOH A 167 385 167 HOH HOH . G 5 HOH A 168 386 168 HOH HOH . G 5 HOH A 169 387 169 HOH HOH . G 5 HOH A 170 388 170 HOH HOH . G 5 HOH A 171 389 171 HOH HOH . G 5 HOH A 172 390 172 HOH HOH . G 5 HOH A 173 391 173 HOH HOH . G 5 HOH A 174 392 174 HOH HOH . G 5 HOH A 175 393 175 HOH HOH . G 5 HOH A 176 394 176 HOH HOH . G 5 HOH A 177 395 177 HOH HOH . G 5 HOH A 178 396 178 HOH HOH . G 5 HOH A 179 397 179 HOH HOH . G 5 HOH A 180 398 180 HOH HOH . G 5 HOH A 181 399 181 HOH HOH . G 5 HOH A 182 400 182 HOH HOH . G 5 HOH A 183 401 183 HOH HOH . G 5 HOH A 184 402 184 HOH HOH . G 5 HOH A 185 403 185 HOH HOH . G 5 HOH A 186 404 186 HOH HOH . G 5 HOH A 187 405 187 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 -25.809 10.879 -20.902 1 26.47 ? PB ADP 214 A 1 HETATM 2 O O1B ADP . . . B 2 -25.401 9.48 -20.476 1 26.73 ? O1B ADP 214 A 1 HETATM 3 O O2B ADP . . . B 2 -25.358 11.183 -22.328 1 28.41 ? O2B ADP 214 A 1 HETATM 4 O O3B ADP . . . B 2 -27.347 11.107 -20.711 1 27.35 ? O3B ADP 214 A 1 HETATM 5 P PA ADP . . . B 2 -24.058 11.824 -18.835 1 26.33 ? PA ADP 214 A 1 HETATM 6 O O1A ADP . . . B 2 -24.305 10.581 -18.015 1 25.84 ? O1A ADP 214 A 1 HETATM 7 O O2A ADP . . . B 2 -23.913 13.117 -18.104 1 27.26 ? O2A ADP 214 A 1 HETATM 8 O O3A ADP . . . B 2 -25.125 11.97 -19.964 1 26.73 ? O3A ADP 214 A 1 HETATM 9 O O5' ADP . . . B 2 -22.67 11.554 -19.603 1 27.07 ? O5' ADP 214 A 1 HETATM 10 C C5' ADP . . . B 2 -22.285 12.645 -20.457 1 26.66 ? C5' ADP 214 A 1 HETATM 11 C C4' ADP . . . B 2 -21.433 12.082 -21.611 1 26.44 ? C4' ADP 214 A 1 HETATM 12 O O4' ADP . . . B 2 -20.133 11.742 -21.103 1 26.48 ? O4' ADP 214 A 1 HETATM 13 C C3' ADP . . . B 2 -22.008 10.83 -22.264 1 27.17 ? C3' ADP 214 A 1 HETATM 14 O O3' ADP . . . B 2 -22.968 11.176 -23.269 1 28.97 ? O3' ADP 214 A 1 HETATM 15 C C2' ADP . . . B 2 -20.729 10.243 -22.957 1 27.14 ? C2' ADP 214 A 1 HETATM 16 O O2' ADP . . . B 2 -20.403 10.956 -24.194 1 29.39 ? O2' ADP 214 A 1 HETATM 17 C C1' ADP . . . B 2 -19.69 10.597 -21.911 1 26.41 ? C1' ADP 214 A 1 HETATM 18 N N9 ADP . . . B 2 -19.323 9.486 -21.052 1 25.38 ? N9 ADP 214 A 1 HETATM 19 C C8 ADP . . . B 2 -19.502 9.405 -19.641 1 25.49 ? C8 ADP 214 A 1 HETATM 20 N N7 ADP . . . B 2 -18.99 8.234 -19.182 1 24.12 ? N7 ADP 214 A 1 HETATM 21 C C5 ADP . . . B 2 -18.507 7.569 -20.291 1 23.99 ? C5 ADP 214 A 1 HETATM 22 C C6 ADP . . . B 2 -17.86 6.264 -20.431 1 24.32 ? C6 ADP 214 A 1 HETATM 23 N N6 ADP . . . B 2 -17.668 5.441 -19.373 1 24.2 ? N6 ADP 214 A 1 HETATM 24 N N1 ADP . . . B 2 -17.45 5.883 -21.671 1 24.52 ? N1 ADP 214 A 1 HETATM 25 C C2 ADP . . . B 2 -17.674 6.718 -22.746 1 25.04 ? C2 ADP 214 A 1 HETATM 26 N N3 ADP . . . B 2 -18.291 7.948 -22.735 1 24.58 ? N3 ADP 214 A 1 HETATM 27 C C4 ADP . . . B 2 -18.675 8.326 -21.46 1 24.29 ? C4 ADP 214 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #