data_3PKE
#
_model_server_result.job_id            mhkhB0INganYEb2tNhBltA 
_model_server_result.datetime_utc      '2025-01-11 03:34:44' 
_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          3pke 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":288}' 
#
_entry.id    3PKE 
#
_exptl.entry_id    3PKE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              58.693 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NICKEL (II) ION' 
_entity.pdbx_number_of_molecules    2 
_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            3PKE 
_cell.length_a            105.454 
_cell.length_b            105.454 
_cell.length_c            50.124 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3PKE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
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 trimeric 3 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 1,2,3 
#
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_455 -y-1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -105.454 0 0 
3 'crystal symmetry operation' 3_445 -x+y-1,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -52.727 -91.325843 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D 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
metalc ? metalc1 A OD1 ASP 131 A ASP 131 1_555 D NI NI . A NI 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc2 A OD2 ASP 131 A ASP 131 1_555 D NI NI . A NI 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc3 A OD1 ASP 142 A ASP 142 1_555 C NI NI . A NI 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc4 A OD2 ASP 142 A ASP 142 1_555 D NI NI . A NI 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? 
metalc ? metalc5 A NE2 HIS 205 A HIS 205 1_555 C NI NI . A NI 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc6 A OE2 GLU 238 A GLU 238 1_555 C NI NI . A NI 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc7 A OE1 GLU 269 A GLU 269 1_555 C NI NI . A NI 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc8 A OE2 GLU 269 A GLU 269 1_555 D NI NI . A NI 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc9 B O3 Y10 . A Y10 286 1_555 C NI NI . A NI 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc10 B O2 Y10 . A Y10 286 1_555 C NI NI . A NI 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc11 B O3 Y10 . A Y10 286 1_555 D NI NI . A NI 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc12 B O1 Y10 . A Y10 286 1_555 D NI NI . A NI 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
#
_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                     3PKE 
_atom_sites.fract_transf_matrix[1][1]    0.009483 
_atom_sites.fract_transf_matrix[1][2]    0.005475 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01095 
_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]    0.019951 
_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 Y10 A 1 286 1 Y10 Y10 . 
C 3 NI A 1 287 1 NI NI . 
D 3 NI A 1 288 2 NI NI . 
E 4 CL A 1 289 1 CL CL . 
F 5 SO4 A 1 290 1 SO4 SO4 . 
G 6 HOH A 1 291 1 HOH HOH . 
G 6 HOH A 2 292 2 HOH HOH . 
G 6 HOH A 3 293 3 HOH HOH . 
G 6 HOH A 4 294 4 HOH HOH . 
G 6 HOH A 5 295 5 HOH HOH . 
G 6 HOH A 6 296 6 HOH HOH . 
G 6 HOH A 7 297 7 HOH HOH . 
G 6 HOH A 8 298 8 HOH HOH . 
G 6 HOH A 9 299 9 HOH HOH . 
G 6 HOH A 10 300 10 HOH HOH . 
G 6 HOH A 11 301 11 HOH HOH . 
G 6 HOH A 12 302 12 HOH HOH . 
G 6 HOH A 13 303 13 HOH HOH . 
G 6 HOH A 14 304 14 HOH HOH . 
G 6 HOH A 15 305 15 HOH HOH . 
G 6 HOH A 16 306 16 HOH HOH . 
G 6 HOH A 17 307 17 HOH HOH . 
G 6 HOH A 18 308 18 HOH HOH . 
G 6 HOH A 19 309 19 HOH HOH . 
G 6 HOH A 20 310 20 HOH HOH . 
G 6 HOH A 21 311 21 HOH HOH . 
G 6 HOH A 22 312 22 HOH HOH . 
G 6 HOH A 23 313 23 HOH HOH . 
G 6 HOH A 24 314 24 HOH HOH . 
G 6 HOH A 25 315 25 HOH HOH . 
G 6 HOH A 26 316 26 HOH HOH . 
G 6 HOH A 27 317 27 HOH HOH . 
G 6 HOH A 28 318 28 HOH HOH . 
G 6 HOH A 29 319 29 HOH HOH . 
G 6 HOH A 30 320 30 HOH HOH . 
G 6 HOH A 31 321 31 HOH HOH . 
G 6 HOH A 32 322 32 HOH HOH . 
G 6 HOH A 33 323 33 HOH HOH . 
G 6 HOH A 34 324 34 HOH HOH . 
G 6 HOH A 35 325 35 HOH HOH . 
G 6 HOH A 36 326 36 HOH HOH . 
G 6 HOH A 37 327 37 HOH HOH . 
G 6 HOH A 38 328 38 HOH HOH . 
G 6 HOH A 39 329 39 HOH HOH . 
G 6 HOH A 40 330 40 HOH HOH . 
G 6 HOH A 41 331 41 HOH HOH . 
G 6 HOH A 42 332 42 HOH HOH . 
G 6 HOH A 43 333 43 HOH HOH . 
G 6 HOH A 44 334 44 HOH HOH . 
G 6 HOH A 45 335 45 HOH HOH . 
G 6 HOH A 46 336 46 HOH HOH . 
G 6 HOH A 47 337 47 HOH HOH . 
G 6 HOH A 48 338 48 HOH HOH . 
G 6 HOH A 49 339 49 HOH HOH . 
G 6 HOH A 50 340 50 HOH HOH . 
G 6 HOH A 51 341 51 HOH HOH . 
G 6 HOH A 52 342 52 HOH HOH . 
G 6 HOH A 53 343 53 HOH HOH . 
G 6 HOH A 54 344 54 HOH HOH . 
G 6 HOH A 55 345 55 HOH HOH . 
G 6 HOH A 56 346 56 HOH HOH . 
G 6 HOH A 57 347 57 HOH HOH . 
G 6 HOH A 58 348 58 HOH HOH . 
G 6 HOH A 59 349 59 HOH HOH . 
G 6 HOH A 60 350 60 HOH HOH . 
G 6 HOH A 61 351 61 HOH HOH . 
G 6 HOH A 62 352 62 HOH HOH . 
G 6 HOH A 63 353 63 HOH HOH . 
G 6 HOH A 64 354 64 HOH HOH . 
G 6 HOH A 65 355 65 HOH HOH . 
G 6 HOH A 66 356 66 HOH HOH . 
G 6 HOH A 67 357 67 HOH HOH . 
G 6 HOH A 68 358 68 HOH HOH . 
G 6 HOH A 69 359 69 HOH HOH . 
G 6 HOH A 70 360 70 HOH HOH . 
G 6 HOH A 71 361 71 HOH HOH . 
G 6 HOH A 72 362 72 HOH HOH . 
G 6 HOH A 73 363 73 HOH HOH . 
G 6 HOH A 74 364 74 HOH HOH . 
G 6 HOH A 75 365 75 HOH HOH . 
G 6 HOH A 76 366 76 HOH HOH . 
G 6 HOH A 77 367 77 HOH HOH . 
G 6 HOH A 78 368 78 HOH HOH . 
G 6 HOH A 79 369 79 HOH HOH . 
G 6 HOH A 80 370 80 HOH HOH . 
G 6 HOH A 81 371 81 HOH HOH . 
G 6 HOH A 82 372 82 HOH HOH . 
G 6 HOH A 83 373 83 HOH HOH . 
G 6 HOH A 84 374 84 HOH HOH . 
G 6 HOH A 85 375 85 HOH HOH . 
G 6 HOH A 86 376 86 HOH HOH . 
G 6 HOH A 87 377 87 HOH HOH . 
G 6 HOH A 88 378 88 HOH HOH . 
G 6 HOH A 89 379 89 HOH HOH . 
G 6 HOH A 90 380 90 HOH HOH . 
G 6 HOH A 91 381 91 HOH HOH . 
G 6 HOH A 92 382 92 HOH HOH . 
G 6 HOH A 93 383 93 HOH HOH . 
G 6 HOH A 94 384 94 HOH HOH . 
G 6 HOH A 95 385 95 HOH HOH . 
G 6 HOH A 96 386 96 HOH HOH . 
G 6 HOH A 97 387 97 HOH HOH . 
G 6 HOH A 98 388 98 HOH HOH . 
G 6 HOH A 99 389 99 HOH HOH . 
G 6 HOH A 100 390 100 HOH HOH . 
G 6 HOH A 101 391 101 HOH HOH . 
G 6 HOH A 102 392 102 HOH HOH . 
G 6 HOH A 103 393 103 HOH HOH . 
G 6 HOH A 104 394 104 HOH HOH . 
G 6 HOH A 105 395 105 HOH HOH . 
G 6 HOH A 106 396 106 HOH HOH . 
G 6 HOH A 107 397 107 HOH HOH . 
G 6 HOH A 108 398 108 HOH HOH . 
G 6 HOH A 109 399 109 HOH HOH . 
G 6 HOH A 110 400 110 HOH HOH . 
G 6 HOH A 111 401 111 HOH HOH . 
G 6 HOH A 112 402 112 HOH HOH . 
G 6 HOH A 113 403 113 HOH HOH . 
G 6 HOH A 114 404 114 HOH HOH . 
G 6 HOH A 115 405 115 HOH HOH . 
G 6 HOH A 116 406 116 HOH HOH . 
G 6 HOH A 117 407 117 HOH HOH . 
G 6 HOH A 118 408 118 HOH HOH . 
G 6 HOH A 119 409 119 HOH HOH . 
G 6 HOH A 120 410 120 HOH HOH . 
G 6 HOH A 121 411 121 HOH HOH . 
G 6 HOH A 122 412 122 HOH HOH . 
G 6 HOH A 123 413 123 HOH HOH . 
G 6 HOH A 124 414 124 HOH HOH . 
G 6 HOH A 125 415 125 HOH HOH . 
G 6 HOH A 126 416 126 HOH HOH . 
G 6 HOH A 127 417 127 HOH HOH . 
G 6 HOH A 128 418 128 HOH HOH . 
G 6 HOH A 129 419 129 HOH HOH . 
G 6 HOH A 130 420 130 HOH HOH . 
G 6 HOH A 131 421 131 HOH HOH . 
G 6 HOH A 132 422 132 HOH HOH . 
G 6 HOH A 133 423 133 HOH HOH . 
G 6 HOH A 134 424 134 HOH HOH . 
G 6 HOH A 135 425 135 HOH HOH . 
G 6 HOH A 136 426 136 HOH HOH . 
G 6 HOH A 137 427 137 HOH HOH . 
G 6 HOH A 138 428 138 HOH HOH . 
G 6 HOH A 139 429 139 HOH HOH . 
G 6 HOH A 140 430 140 HOH HOH . 
G 6 HOH A 141 431 141 HOH HOH . 
G 6 HOH A 142 432 142 HOH HOH . 
G 6 HOH A 143 433 143 HOH HOH . 
G 6 HOH A 144 434 144 HOH HOH . 
G 6 HOH A 145 435 145 HOH HOH . 
G 6 HOH A 146 436 146 HOH HOH . 
G 6 HOH A 147 437 147 HOH HOH . 
G 6 HOH A 148 438 148 HOH HOH . 
G 6 HOH A 149 439 149 HOH HOH . 
G 6 HOH A 150 440 150 HOH HOH . 
G 6 HOH A 151 441 151 HOH HOH . 
G 6 HOH A 152 442 152 HOH HOH . 
G 6 HOH A 153 443 153 HOH HOH . 
G 6 HOH A 154 444 154 HOH HOH . 
G 6 HOH A 155 445 155 HOH HOH . 
G 6 HOH A 156 446 156 HOH HOH . 
G 6 HOH A 157 447 157 HOH HOH . 
G 6 HOH A 158 448 158 HOH HOH . 
G 6 HOH A 159 449 159 HOH HOH . 
G 6 HOH A 160 450 160 HOH HOH . 
G 6 HOH A 161 451 161 HOH HOH . 
G 6 HOH A 162 452 162 HOH HOH . 
G 6 HOH A 163 453 163 HOH HOH . 
G 6 HOH A 164 454 164 HOH HOH . 
G 6 HOH A 165 455 165 HOH HOH . 
G 6 HOH A 166 456 166 HOH HOH . 
G 6 HOH A 167 457 167 HOH HOH . 
G 6 HOH A 168 458 168 HOH HOH . 
G 6 HOH A 169 459 169 HOH HOH . 
G 6 HOH A 170 460 170 HOH HOH . 
G 6 HOH A 171 461 171 HOH HOH . 
G 6 HOH A 172 462 172 HOH HOH . 
G 6 HOH A 173 463 173 HOH HOH . 
G 6 HOH A 174 464 174 HOH HOH . 
G 6 HOH A 175 465 175 HOH HOH . 
G 6 HOH A 176 466 176 HOH HOH . 
G 6 HOH A 177 467 177 HOH HOH . 
G 6 HOH A 178 468 178 HOH HOH . 
G 6 HOH A 179 469 179 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       3 
_atom_site.Cartn_x               -31.467 
_atom_site.Cartn_y               -30.505 
_atom_site.Cartn_z               -0.592 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        7.15 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           288 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#