data_3VJ6 # _model_server_result.job_id FRXWZV02cRjNtVplxeIY2g _model_server_result.datetime_utc '2024-11-14 13:47:23' _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 3vj6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":278}' # _entry.id 3VJ6 # _exptl.entry_id 3VJ6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 4 _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 3VJ6 _cell.length_a 59.268 _cell.length_b 72.833 _cell.length_c 95.844 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VJ6 _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N 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 disulf ? disulf1 A SG CYS 101 A CYS 101 1_555 A SG CYS 164 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf2 A SG CYS 203 A CYS 203 1_555 A SG CYS 259 A CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 B SG CYS 26 B CYS 25 1_555 B SG CYS 81 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A NE2 HIS 260 A HIS 260 1_555 D NI NI . A NI 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc2 D NI NI . A NI 278 1_555 H O HOH . A HOH 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc3 D NI NI . A NI 278 1_555 H O HOH . A HOH 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 D NI NI . A NI 278 1_555 H O HOH . A HOH 457 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc5 E NI NI . A NI 279 1_555 H O HOH . A HOH 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc6 E NI NI . A NI 279 1_555 I O HOH . B HOH 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc7 B NE2 HIS 35 B HIS 34 1_555 F NI NI . B NI 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc8 B NE2 HIS 68 B HIS 67 1_555 G NI NI . B NI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc9 F NI NI . B NI 100 1_555 I O HOH . B HOH 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc10 F NI NI . B NI 100 1_555 I O HOH . B HOH 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc11 F NI NI . B NI 100 1_555 I O HOH . B HOH 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc12 G NI NI . B NI 101 1_555 I O HOH . B HOH 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc13 G NI NI . B NI 101 1_555 I O HOH . B HOH 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc14 G NI NI . B NI 101 1_555 I O HOH . B HOH 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? # _chem_comp.formula 'Ni 2' _chem_comp.formula_weight 58.693 _chem_comp.id NI _chem_comp.mon_nstd_flag . _chem_comp.name 'NICKEL (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3VJ6 _atom_sites.fract_transf_matrix[1][1] 0.016873 _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] 0.01373 _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] 0.010434 _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 D 4 NI A 1 278 1 NI NI . E 4 NI A 1 279 4 NI NI . F 4 NI B 1 100 2 NI NI . G 4 NI B 1 101 3 NI NI . H 5 HOH A 1 280 1 HOH HOH . H 5 HOH A 2 281 2 HOH HOH . H 5 HOH A 3 282 3 HOH HOH . H 5 HOH A 4 283 5 HOH HOH . H 5 HOH A 5 284 6 HOH HOH . H 5 HOH A 6 285 7 HOH HOH . H 5 HOH A 7 286 8 HOH HOH . H 5 HOH A 8 287 9 HOH HOH . H 5 HOH A 9 288 10 HOH HOH . H 5 HOH A 10 289 11 HOH HOH . H 5 HOH A 11 290 12 HOH HOH . H 5 HOH A 12 291 13 HOH HOH . H 5 HOH A 13 292 14 HOH HOH . H 5 HOH A 14 293 15 HOH HOH . H 5 HOH A 15 294 16 HOH HOH . H 5 HOH A 16 295 17 HOH HOH . H 5 HOH A 17 296 18 HOH HOH . H 5 HOH A 18 297 19 HOH HOH . H 5 HOH A 19 298 20 HOH HOH . H 5 HOH A 20 299 22 HOH HOH . H 5 HOH A 21 300 23 HOH HOH . H 5 HOH A 22 301 24 HOH HOH . H 5 HOH A 23 302 28 HOH HOH . H 5 HOH A 24 303 30 HOH HOH . H 5 HOH A 25 304 31 HOH HOH . H 5 HOH A 26 305 32 HOH HOH . H 5 HOH A 27 306 33 HOH HOH . H 5 HOH A 28 307 34 HOH HOH . H 5 HOH A 29 308 35 HOH HOH . H 5 HOH A 30 309 36 HOH HOH . H 5 HOH A 31 310 37 HOH HOH . H 5 HOH A 32 311 38 HOH HOH . H 5 HOH A 33 312 40 HOH HOH . H 5 HOH A 34 313 41 HOH HOH . H 5 HOH A 35 314 42 HOH HOH . H 5 HOH A 36 315 43 HOH HOH . H 5 HOH A 37 316 44 HOH HOH . H 5 HOH A 38 317 45 HOH HOH . H 5 HOH A 39 318 48 HOH HOH . H 5 HOH A 40 319 49 HOH HOH . H 5 HOH A 41 320 50 HOH HOH . H 5 HOH A 42 321 53 HOH HOH . H 5 HOH A 43 322 54 HOH HOH . H 5 HOH A 44 323 55 HOH HOH . H 5 HOH A 45 324 56 HOH HOH . H 5 HOH A 46 325 57 HOH HOH . H 5 HOH A 47 326 58 HOH HOH . H 5 HOH A 48 327 59 HOH HOH . H 5 HOH A 49 328 60 HOH HOH . H 5 HOH A 50 329 61 HOH HOH . H 5 HOH A 51 330 62 HOH HOH . H 5 HOH A 52 331 63 HOH HOH . H 5 HOH A 53 332 64 HOH HOH . H 5 HOH A 54 333 65 HOH HOH . H 5 HOH A 55 334 67 HOH HOH . H 5 HOH A 56 335 68 HOH HOH . H 5 HOH A 57 336 69 HOH HOH . H 5 HOH A 58 337 70 HOH HOH . H 5 HOH A 59 338 71 HOH HOH . H 5 HOH A 60 339 74 HOH HOH . H 5 HOH A 61 340 76 HOH HOH . H 5 HOH A 62 341 77 HOH HOH . H 5 HOH A 63 342 78 HOH HOH . H 5 HOH A 64 343 79 HOH HOH . H 5 HOH A 65 344 80 HOH HOH . H 5 HOH A 66 345 81 HOH HOH . H 5 HOH A 67 346 82 HOH HOH . H 5 HOH A 68 347 83 HOH HOH . H 5 HOH A 69 348 84 HOH HOH . H 5 HOH A 70 349 85 HOH HOH . H 5 HOH A 71 350 86 HOH HOH . H 5 HOH A 72 351 88 HOH HOH . H 5 HOH A 73 352 89 HOH HOH . H 5 HOH A 74 353 90 HOH HOH . H 5 HOH A 75 354 91 HOH HOH . H 5 HOH A 76 355 92 HOH HOH . H 5 HOH A 77 356 93 HOH HOH . H 5 HOH A 78 357 94 HOH HOH . H 5 HOH A 79 358 95 HOH HOH . H 5 HOH A 80 359 96 HOH HOH . H 5 HOH A 81 360 97 HOH HOH . H 5 HOH A 82 361 98 HOH HOH . H 5 HOH A 83 362 99 HOH HOH . H 5 HOH A 84 363 100 HOH HOH . H 5 HOH A 85 364 101 HOH HOH . H 5 HOH A 86 365 102 HOH HOH . H 5 HOH A 87 366 103 HOH HOH . H 5 HOH A 88 367 104 HOH HOH . H 5 HOH A 89 368 105 HOH HOH . H 5 HOH A 90 369 106 HOH HOH . H 5 HOH A 91 370 107 HOH HOH . H 5 HOH A 92 371 110 HOH HOH . H 5 HOH A 93 372 111 HOH HOH . H 5 HOH A 94 373 112 HOH HOH . H 5 HOH A 95 374 113 HOH HOH . H 5 HOH A 96 375 114 HOH HOH . H 5 HOH A 97 376 115 HOH HOH . H 5 HOH A 98 377 116 HOH HOH . H 5 HOH A 99 378 117 HOH HOH . H 5 HOH A 100 379 118 HOH HOH . H 5 HOH A 101 380 119 HOH HOH . H 5 HOH A 102 381 120 HOH HOH . H 5 HOH A 103 382 122 HOH HOH . H 5 HOH A 104 383 124 HOH HOH . H 5 HOH A 105 384 125 HOH HOH . H 5 HOH A 106 385 127 HOH HOH . H 5 HOH A 107 386 128 HOH HOH . H 5 HOH A 108 387 129 HOH HOH . H 5 HOH A 109 388 137 HOH HOH . H 5 HOH A 110 389 139 HOH HOH . H 5 HOH A 111 390 140 HOH HOH . H 5 HOH A 112 391 142 HOH HOH . H 5 HOH A 113 392 143 HOH HOH . H 5 HOH A 114 393 144 HOH HOH . H 5 HOH A 115 394 146 HOH HOH . H 5 HOH A 116 395 147 HOH HOH . H 5 HOH A 117 396 148 HOH HOH . H 5 HOH A 118 397 149 HOH HOH . H 5 HOH A 119 398 150 HOH HOH . H 5 HOH A 120 399 151 HOH HOH . H 5 HOH A 121 400 153 HOH HOH . H 5 HOH A 122 401 155 HOH HOH . H 5 HOH A 123 402 156 HOH HOH . H 5 HOH A 124 403 157 HOH HOH . H 5 HOH A 125 404 158 HOH HOH . H 5 HOH A 126 405 159 HOH HOH . H 5 HOH A 127 406 160 HOH HOH . H 5 HOH A 128 407 161 HOH HOH . H 5 HOH A 129 408 162 HOH HOH . H 5 HOH A 130 409 163 HOH HOH . H 5 HOH A 131 410 165 HOH HOH . H 5 HOH A 132 411 166 HOH HOH . H 5 HOH A 133 412 167 HOH HOH . H 5 HOH A 134 413 172 HOH HOH . H 5 HOH A 135 414 173 HOH HOH . H 5 HOH A 136 415 174 HOH HOH . H 5 HOH A 137 416 175 HOH HOH . H 5 HOH A 138 417 176 HOH HOH . H 5 HOH A 139 418 177 HOH HOH . H 5 HOH A 140 419 179 HOH HOH . H 5 HOH A 141 420 180 HOH HOH . H 5 HOH A 142 421 182 HOH HOH . H 5 HOH A 143 422 183 HOH HOH . H 5 HOH A 144 423 185 HOH HOH . H 5 HOH A 145 424 186 HOH HOH . H 5 HOH A 146 425 189 HOH HOH . H 5 HOH A 147 426 190 HOH HOH . H 5 HOH A 148 427 191 HOH HOH . H 5 HOH A 149 428 192 HOH HOH . H 5 HOH A 150 429 193 HOH HOH . H 5 HOH A 151 430 196 HOH HOH . H 5 HOH A 152 431 199 HOH HOH . H 5 HOH A 153 432 200 HOH HOH . H 5 HOH A 154 433 201 HOH HOH . H 5 HOH A 155 434 202 HOH HOH . H 5 HOH A 156 435 203 HOH HOH . H 5 HOH A 157 436 204 HOH HOH . H 5 HOH A 158 437 205 HOH HOH . H 5 HOH A 159 438 208 HOH HOH . H 5 HOH A 160 439 210 HOH HOH . H 5 HOH A 161 440 211 HOH HOH . H 5 HOH A 162 441 212 HOH HOH . H 5 HOH A 163 442 215 HOH HOH . H 5 HOH A 164 443 217 HOH HOH . H 5 HOH A 165 444 218 HOH HOH . H 5 HOH A 166 445 220 HOH HOH . H 5 HOH A 167 446 221 HOH HOH . H 5 HOH A 168 447 222 HOH HOH . H 5 HOH A 169 448 223 HOH HOH . H 5 HOH A 170 449 224 HOH HOH . H 5 HOH A 171 450 225 HOH HOH . H 5 HOH A 172 451 228 HOH HOH . H 5 HOH A 173 452 229 HOH HOH . H 5 HOH A 174 453 231 HOH HOH . H 5 HOH A 175 454 232 HOH HOH . H 5 HOH A 176 455 233 HOH HOH . H 5 HOH A 177 456 234 HOH HOH . H 5 HOH A 178 457 236 HOH HOH . H 5 HOH A 179 458 237 HOH HOH . H 5 HOH A 180 459 241 HOH HOH . H 5 HOH A 181 460 244 HOH HOH . H 5 HOH A 182 461 246 HOH HOH . H 5 HOH A 183 462 248 HOH HOH . H 5 HOH A 184 463 249 HOH HOH . H 5 HOH A 185 464 250 HOH HOH . H 5 HOH A 186 465 251 HOH HOH . H 5 HOH A 187 466 252 HOH HOH . H 5 HOH A 188 467 253 HOH HOH . H 5 HOH A 189 468 254 HOH HOH . H 5 HOH A 190 469 256 HOH HOH . H 5 HOH A 191 470 257 HOH HOH . H 5 HOH A 192 471 258 HOH HOH . H 5 HOH A 193 472 259 HOH HOH . H 5 HOH A 194 473 260 HOH HOH . H 5 HOH A 195 474 261 HOH HOH . H 5 HOH A 196 475 262 HOH HOH . H 5 HOH A 197 476 263 HOH HOH . I 5 HOH B 1 102 4 HOH HOH . I 5 HOH B 2 103 21 HOH HOH . I 5 HOH B 3 104 26 HOH HOH . I 5 HOH B 4 105 27 HOH HOH . I 5 HOH B 5 106 29 HOH HOH . I 5 HOH B 6 107 39 HOH HOH . I 5 HOH B 7 108 108 HOH HOH . I 5 HOH B 8 109 109 HOH HOH . I 5 HOH B 9 110 46 HOH HOH . I 5 HOH B 10 111 47 HOH HOH . I 5 HOH B 11 112 51 HOH HOH . I 5 HOH B 12 113 52 HOH HOH . I 5 HOH B 13 114 66 HOH HOH . I 5 HOH B 14 115 72 HOH HOH . I 5 HOH B 15 116 73 HOH HOH . I 5 HOH B 16 117 75 HOH HOH . I 5 HOH B 17 118 87 HOH HOH . I 5 HOH B 18 121 121 HOH HOH . I 5 HOH B 19 123 123 HOH HOH . I 5 HOH B 20 126 126 HOH HOH . I 5 HOH B 21 130 130 HOH HOH . I 5 HOH B 22 131 131 HOH HOH . I 5 HOH B 23 132 132 HOH HOH . I 5 HOH B 24 133 133 HOH HOH . I 5 HOH B 25 134 134 HOH HOH . I 5 HOH B 26 135 135 HOH HOH . I 5 HOH B 27 136 136 HOH HOH . I 5 HOH B 28 138 138 HOH HOH . I 5 HOH B 29 145 145 HOH HOH . I 5 HOH B 30 154 154 HOH HOH . I 5 HOH B 31 164 164 HOH HOH . I 5 HOH B 32 168 168 HOH HOH . I 5 HOH B 33 169 169 HOH HOH . I 5 HOH B 34 170 170 HOH HOH . I 5 HOH B 35 171 171 HOH HOH . I 5 HOH B 36 178 178 HOH HOH . I 5 HOH B 37 181 181 HOH HOH . I 5 HOH B 38 184 184 HOH HOH . I 5 HOH B 39 187 187 HOH HOH . I 5 HOH B 40 188 188 HOH HOH . I 5 HOH B 41 195 195 HOH HOH . I 5 HOH B 42 197 197 HOH HOH . I 5 HOH B 43 198 198 HOH HOH . I 5 HOH B 44 206 206 HOH HOH . I 5 HOH B 45 207 207 HOH HOH . I 5 HOH B 46 209 209 HOH HOH . I 5 HOH B 47 213 213 HOH HOH . I 5 HOH B 48 214 214 HOH HOH . I 5 HOH B 49 216 216 HOH HOH . I 5 HOH B 50 226 226 HOH HOH . I 5 HOH B 51 227 227 HOH HOH . I 5 HOH B 52 235 235 HOH HOH . I 5 HOH B 53 238 238 HOH HOH . I 5 HOH B 54 239 239 HOH HOH . I 5 HOH B 55 240 240 HOH HOH . I 5 HOH B 56 242 242 HOH HOH . I 5 HOH B 57 243 243 HOH HOH . I 5 HOH B 58 245 245 HOH HOH . I 5 HOH B 59 247 247 HOH HOH . I 5 HOH B 60 255 255 HOH HOH . J 5 HOH P 1 25 25 HOH HOH . J 5 HOH P 2 141 141 HOH HOH . J 5 HOH P 3 152 152 HOH HOH . J 5 HOH P 4 194 194 HOH HOH . J 5 HOH P 5 219 219 HOH HOH . J 5 HOH P 6 230 230 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NI _atom_site.label_atom_id NI _atom_site.label_comp_id NI _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x -3.118 _atom_site.Cartn_y 29.855 _atom_site.Cartn_z 23.051 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 19.93 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 278 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #