data_3MIB
#
_model_server_result.job_id            lQiyyeAEWDZoVzzxcTSLgA 
_model_server_result.datetime_utc      '2025-01-11 10:50:22' 
_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          3mib 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":359}' 
#
_entry.id    3MIB 
#
_exptl.entry_id    3MIB 
_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    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            3MIB 
_cell.length_a            68.612 
_cell.length_b            68.617 
_cell.length_c            80.254 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3MIB 
_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,F,G,H,I,J,K 
_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                      3 
_struct_asym.id                             D 
_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
disulf ? disulf1 A SG CYS 5 A CYS 47 1_555 A SG CYS 144 A CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf2 A SG CYS 39 A CYS 81 1_555 A SG CYS 84 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 72 A CYS 114 1_555 A SG CYS 89 A CYS 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf4 A SG CYS 185 A CYS 227 1_555 A SG CYS 292 A CYS 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf5 A SG CYS 251 A CYS 293 1_555 A SG CYS 273 A CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc1 E O1 NO2 . A NO2 1 1_555 C CU CU . A CU 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? 
metalc ? metalc2 E O2 NO2 . A NO2 1 1_555 C CU CU . A CU 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? 
metalc ? metalc3 F O2 NO2 . A NO2 2 1_555 D NI NI . A NI 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc4 F O1 NO2 . A NO2 2 1_555 D NI NI . A NI 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
metalc ? metalc5 F N NO2 . A NO2 2 1_555 D NI NI . A NI 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? 
metalc ? metalc6 A ND1 HIS 65 A HIS 107 1_555 B CU CU . A CU 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc7 A ND1 HIS 66 A HIS 108 1_555 B CU CU . A CU 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc8 A ND1 HIS 130 A HIS 172 1_555 B CU CU . A CU 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc9 A NE2 HIS 193 A HIS 235 1_555 D NI NI . A NI 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc10 A NE2 HIS 200 A HIS 242 1_555 C CU CU . A CU 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc11 A NE2 HIS 202 A HIS 244 1_555 C CU CU . A CU 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc12 A SD MET 272 A MET 314 1_555 C CU CU . A CU 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? 
metalc ? metalc13 D NI NI . A NI 359 1_555 K O HOH . A HOH 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
metalc ? metalc14 D NI NI . A NI 359 1_555 K O HOH . A HOH 486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? 
#
_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                     3MIB 
_atom_sites.fract_transf_matrix[1][1]    0.014575 
_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]    0.014574 
_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]    0.01246 
_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 CU A 1 357 357 CU CU . 
C 2 CU A 1 358 358 CU CU . 
D 3 NI A 1 359 359 NI NI . 
E 4 NO2 A 1 1 1 NO2 NO2 . 
F 4 NO2 A 1 2 2 NO2 NO2 . 
G 4 NO2 A 1 3 3 NO2 NO2 . 
H 5 GOL A 1 360 1 GOL GOL . 
I 5 GOL A 1 361 2 GOL GOL . 
J 5 GOL A 1 362 3 GOL GOL . 
K 6 HOH A 1 4 4 HOH HOH . 
K 6 HOH A 2 5 5 HOH HOH . 
K 6 HOH A 3 6 6 HOH HOH . 
K 6 HOH A 4 7 7 HOH HOH . 
K 6 HOH A 5 8 8 HOH HOH . 
K 6 HOH A 6 9 9 HOH HOH . 
K 6 HOH A 7 10 10 HOH HOH . 
K 6 HOH A 8 11 11 HOH HOH . 
K 6 HOH A 9 12 12 HOH HOH . 
K 6 HOH A 10 13 13 HOH HOH . 
K 6 HOH A 11 14 14 HOH HOH . 
K 6 HOH A 12 15 15 HOH HOH . 
K 6 HOH A 13 16 16 HOH HOH . 
K 6 HOH A 14 17 17 HOH HOH . 
K 6 HOH A 15 18 18 HOH HOH . 
K 6 HOH A 16 19 19 HOH HOH . 
K 6 HOH A 17 20 20 HOH HOH . 
K 6 HOH A 18 21 21 HOH HOH . 
K 6 HOH A 19 22 22 HOH HOH . 
K 6 HOH A 20 23 23 HOH HOH . 
K 6 HOH A 21 24 24 HOH HOH . 
K 6 HOH A 22 25 25 HOH HOH . 
K 6 HOH A 23 27 27 HOH HOH . 
K 6 HOH A 24 28 28 HOH HOH . 
K 6 HOH A 25 29 29 HOH HOH . 
K 6 HOH A 26 30 30 HOH HOH . 
K 6 HOH A 27 31 31 HOH HOH . 
K 6 HOH A 28 32 32 HOH HOH . 
K 6 HOH A 29 33 33 HOH HOH . 
K 6 HOH A 30 34 34 HOH HOH . 
K 6 HOH A 31 35 35 HOH HOH . 
K 6 HOH A 32 36 36 HOH HOH . 
K 6 HOH A 33 37 37 HOH HOH . 
K 6 HOH A 34 38 38 HOH HOH . 
K 6 HOH A 35 39 39 HOH HOH . 
K 6 HOH A 36 40 40 HOH HOH . 
K 6 HOH A 37 41 41 HOH HOH . 
K 6 HOH A 38 42 42 HOH HOH . 
K 6 HOH A 39 363 1 HOH HOH . 
K 6 HOH A 40 364 2 HOH HOH . 
K 6 HOH A 41 365 3 HOH HOH . 
K 6 HOH A 42 366 43 HOH HOH . 
K 6 HOH A 43 367 44 HOH HOH . 
K 6 HOH A 44 368 45 HOH HOH . 
K 6 HOH A 45 369 46 HOH HOH . 
K 6 HOH A 46 370 47 HOH HOH . 
K 6 HOH A 47 371 48 HOH HOH . 
K 6 HOH A 48 372 49 HOH HOH . 
K 6 HOH A 49 373 50 HOH HOH . 
K 6 HOH A 50 374 51 HOH HOH . 
K 6 HOH A 51 375 52 HOH HOH . 
K 6 HOH A 52 376 53 HOH HOH . 
K 6 HOH A 53 377 54 HOH HOH . 
K 6 HOH A 54 378 55 HOH HOH . 
K 6 HOH A 55 379 56 HOH HOH . 
K 6 HOH A 56 380 57 HOH HOH . 
K 6 HOH A 57 381 58 HOH HOH . 
K 6 HOH A 58 382 59 HOH HOH . 
K 6 HOH A 59 383 60 HOH HOH . 
K 6 HOH A 60 384 61 HOH HOH . 
K 6 HOH A 61 385 62 HOH HOH . 
K 6 HOH A 62 386 63 HOH HOH . 
K 6 HOH A 63 387 64 HOH HOH . 
K 6 HOH A 64 388 65 HOH HOH . 
K 6 HOH A 65 389 67 HOH HOH . 
K 6 HOH A 66 390 69 HOH HOH . 
K 6 HOH A 67 391 70 HOH HOH . 
K 6 HOH A 68 392 71 HOH HOH . 
K 6 HOH A 69 393 72 HOH HOH . 
K 6 HOH A 70 394 73 HOH HOH . 
K 6 HOH A 71 395 74 HOH HOH . 
K 6 HOH A 72 396 75 HOH HOH . 
K 6 HOH A 73 397 76 HOH HOH . 
K 6 HOH A 74 398 77 HOH HOH . 
K 6 HOH A 75 399 78 HOH HOH . 
K 6 HOH A 76 400 79 HOH HOH . 
K 6 HOH A 77 401 80 HOH HOH . 
K 6 HOH A 78 402 81 HOH HOH . 
K 6 HOH A 79 403 82 HOH HOH . 
K 6 HOH A 80 404 83 HOH HOH . 
K 6 HOH A 81 405 84 HOH HOH . 
K 6 HOH A 82 406 85 HOH HOH . 
K 6 HOH A 83 407 86 HOH HOH . 
K 6 HOH A 84 408 87 HOH HOH . 
K 6 HOH A 85 409 88 HOH HOH . 
K 6 HOH A 86 410 89 HOH HOH . 
K 6 HOH A 87 411 90 HOH HOH . 
K 6 HOH A 88 412 91 HOH HOH . 
K 6 HOH A 89 413 92 HOH HOH . 
K 6 HOH A 90 414 93 HOH HOH . 
K 6 HOH A 91 415 95 HOH HOH . 
K 6 HOH A 92 416 96 HOH HOH . 
K 6 HOH A 93 417 97 HOH HOH . 
K 6 HOH A 94 418 98 HOH HOH . 
K 6 HOH A 95 419 99 HOH HOH . 
K 6 HOH A 96 420 100 HOH HOH . 
K 6 HOH A 97 421 101 HOH HOH . 
K 6 HOH A 98 422 102 HOH HOH . 
K 6 HOH A 99 423 103 HOH HOH . 
K 6 HOH A 100 424 104 HOH HOH . 
K 6 HOH A 101 425 105 HOH HOH . 
K 6 HOH A 102 426 106 HOH HOH . 
K 6 HOH A 103 427 107 HOH HOH . 
K 6 HOH A 104 428 108 HOH HOH . 
K 6 HOH A 105 429 109 HOH HOH . 
K 6 HOH A 106 430 110 HOH HOH . 
K 6 HOH A 107 431 111 HOH HOH . 
K 6 HOH A 108 432 112 HOH HOH . 
K 6 HOH A 109 433 113 HOH HOH . 
K 6 HOH A 110 434 114 HOH HOH . 
K 6 HOH A 111 435 115 HOH HOH . 
K 6 HOH A 112 436 116 HOH HOH . 
K 6 HOH A 113 437 117 HOH HOH . 
K 6 HOH A 114 438 118 HOH HOH . 
K 6 HOH A 115 439 119 HOH HOH . 
K 6 HOH A 116 440 120 HOH HOH . 
K 6 HOH A 117 441 121 HOH HOH . 
K 6 HOH A 118 442 122 HOH HOH . 
K 6 HOH A 119 443 123 HOH HOH . 
K 6 HOH A 120 444 124 HOH HOH . 
K 6 HOH A 121 445 125 HOH HOH . 
K 6 HOH A 122 446 126 HOH HOH . 
K 6 HOH A 123 447 127 HOH HOH . 
K 6 HOH A 124 448 128 HOH HOH . 
K 6 HOH A 125 449 129 HOH HOH . 
K 6 HOH A 126 450 130 HOH HOH . 
K 6 HOH A 127 451 131 HOH HOH . 
K 6 HOH A 128 452 132 HOH HOH . 
K 6 HOH A 129 453 133 HOH HOH . 
K 6 HOH A 130 454 134 HOH HOH . 
K 6 HOH A 131 455 135 HOH HOH . 
K 6 HOH A 132 456 136 HOH HOH . 
K 6 HOH A 133 457 137 HOH HOH . 
K 6 HOH A 134 458 138 HOH HOH . 
K 6 HOH A 135 459 139 HOH HOH . 
K 6 HOH A 136 460 140 HOH HOH . 
K 6 HOH A 137 461 141 HOH HOH . 
K 6 HOH A 138 462 142 HOH HOH . 
K 6 HOH A 139 463 143 HOH HOH . 
K 6 HOH A 140 464 144 HOH HOH . 
K 6 HOH A 141 465 145 HOH HOH . 
K 6 HOH A 142 466 146 HOH HOH . 
K 6 HOH A 143 467 147 HOH HOH . 
K 6 HOH A 144 468 148 HOH HOH . 
K 6 HOH A 145 469 150 HOH HOH . 
K 6 HOH A 146 470 151 HOH HOH . 
K 6 HOH A 147 471 152 HOH HOH . 
K 6 HOH A 148 472 154 HOH HOH . 
K 6 HOH A 149 473 155 HOH HOH . 
K 6 HOH A 150 474 156 HOH HOH . 
K 6 HOH A 151 475 157 HOH HOH . 
K 6 HOH A 152 476 158 HOH HOH . 
K 6 HOH A 153 477 159 HOH HOH . 
K 6 HOH A 154 478 160 HOH HOH . 
K 6 HOH A 155 479 161 HOH HOH . 
K 6 HOH A 156 480 162 HOH HOH . 
K 6 HOH A 157 481 163 HOH HOH . 
K 6 HOH A 158 482 165 HOH HOH . 
K 6 HOH A 159 483 167 HOH HOH . 
K 6 HOH A 160 484 168 HOH HOH . 
K 6 HOH A 161 485 169 HOH HOH . 
K 6 HOH A 162 486 170 HOH HOH . 
K 6 HOH A 163 487 171 HOH HOH . 
K 6 HOH A 164 488 172 HOH HOH . 
K 6 HOH A 165 489 173 HOH HOH . 
K 6 HOH A 166 490 174 HOH HOH . 
K 6 HOH A 167 491 175 HOH HOH . 
K 6 HOH A 168 492 176 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               46.635 
_atom_site.Cartn_y               7.921 
_atom_site.Cartn_z               31.831 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        51.01 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           359 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           368 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#