data_5F3M # _model_server_result.job_id yo9g00NeL8Adt7JtsEvCtA _model_server_result.datetime_utc '2024-12-16 11:32:03' _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 5f3m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 5F3M # _exptl.entry_id 5F3M _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 90 _cell.entry_id 5F3M _cell.length_a 87.974 _cell.length_b 87.974 _cell.length_c 104.549 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F3M _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,L,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 87.974 0 0 3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 43.987 -43.987 0 4 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 43.987 43.987 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 I 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 covale ? covale1 A C MSE 4 A MSE 1 1_555 A N ASP 5 A ASP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C ASP 11 A ASP 8 1_555 A N MSE 12 A MSE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C MSE 12 A MSE 9 1_555 A N GLU 13 A GLU 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C MSE 4 B MSE 1 1_555 B N ASP 5 B ASP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale5 B C ASP 11 B ASP 8 1_555 B N MSE 12 B MSE 9 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 B C ASP 11 B ASP 8 1_555 B N MSE 12 B MSE 9 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 B C MSE 12 B MSE 9 1_555 B N GLU 13 B GLU 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A NE2 HIS 52 A HIS 49 1_555 D NI NI . A NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc2 A NE2 HIS 52 A HIS 49 1_555 D NI NI . A NI 202 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc3 D NI NI . A NI 202 1_555 N O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc4 D NI NI . A NI 202 1_555 N O HOH . A HOH 301 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc5 D NI NI . A NI 202 1_555 N O HOH . A HOH 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc6 D NI NI . A NI 202 1_555 N O HOH . A HOH 380 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc7 B NE2 HIS 52 B HIS 49 1_555 I NI NI . B NI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc8 B NE2 HIS 52 B HIS 49 1_555 I NI NI . B NI 202 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc9 I NI NI . B NI 202 1_555 O O HOH . B HOH 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc10 I NI NI . B NI 202 1_555 O O HOH . B HOH 370 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc11 I NI NI . B NI 202 1_555 O O HOH . B HOH 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc12 I NI NI . B NI 202 1_555 O O HOH . B HOH 378 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc13 I NI NI . B NI 202 1_555 O O HOH . B HOH 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc14 I NI NI . B NI 202 1_555 O O HOH . B HOH 381 8_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? # _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 5F3M _atom_sites.fract_transf_matrix[1][1] 0.011367 _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] 0.011367 _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] 0.009565 _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 C 2 NEU A 1 201 130 NEU NEU . D 3 NI A 1 202 131 NI NI . E 4 EDO A 1 203 132 EDO EDO . F 4 EDO A 1 204 133 EDO EDO . G 4 EDO A 1 205 135 EDO EDO . H 2 NEU B 1 201 130 NEU NEU . I 3 NI B 1 202 131 NI NI . J 4 EDO B 1 203 132 EDO EDO . K 5 CL B 1 204 133 CL CL . L 6 FMT B 1 205 135 FMT FMT . M 4 EDO B 1 206 137 EDO EDO . N 7 HOH A 1 301 232 HOH HOH . N 7 HOH A 2 302 75 HOH HOH . N 7 HOH A 3 303 21 HOH HOH . N 7 HOH A 4 304 77 HOH HOH . N 7 HOH A 5 305 134 HOH HOH . N 7 HOH A 6 306 69 HOH HOH . N 7 HOH A 7 307 214 HOH HOH . N 7 HOH A 8 308 11 HOH HOH . N 7 HOH A 9 309 166 HOH HOH . N 7 HOH A 10 310 157 HOH HOH . N 7 HOH A 11 311 181 HOH HOH . N 7 HOH A 12 312 7 HOH HOH . N 7 HOH A 13 313 41 HOH HOH . N 7 HOH A 14 314 171 HOH HOH . N 7 HOH A 15 315 228 HOH HOH . N 7 HOH A 16 316 1 HOH HOH . N 7 HOH A 17 317 236 HOH HOH . N 7 HOH A 18 318 125 HOH HOH . N 7 HOH A 19 319 27 HOH HOH . N 7 HOH A 20 320 16 HOH HOH . N 7 HOH A 21 321 168 HOH HOH . N 7 HOH A 22 322 177 HOH HOH . N 7 HOH A 23 323 230 HOH HOH . N 7 HOH A 24 324 154 HOH HOH . N 7 HOH A 25 325 90 HOH HOH . N 7 HOH A 26 326 112 HOH HOH . N 7 HOH A 27 327 32 HOH HOH . N 7 HOH A 28 328 2 HOH HOH . N 7 HOH A 29 329 9 HOH HOH . N 7 HOH A 30 330 156 HOH HOH . N 7 HOH A 31 331 52 HOH HOH . N 7 HOH A 32 332 91 HOH HOH . N 7 HOH A 33 333 66 HOH HOH . N 7 HOH A 34 334 73 HOH HOH . N 7 HOH A 35 335 212 HOH HOH . N 7 HOH A 36 336 144 HOH HOH . N 7 HOH A 37 337 42 HOH HOH . N 7 HOH A 38 338 143 HOH HOH . N 7 HOH A 39 339 60 HOH HOH . N 7 HOH A 40 340 36 HOH HOH . N 7 HOH A 41 341 22 HOH HOH . N 7 HOH A 42 342 153 HOH HOH . N 7 HOH A 43 343 231 HOH HOH . N 7 HOH A 44 344 180 HOH HOH . N 7 HOH A 45 345 179 HOH HOH . N 7 HOH A 46 346 35 HOH HOH . N 7 HOH A 47 347 29 HOH HOH . N 7 HOH A 48 348 146 HOH HOH . N 7 HOH A 49 349 82 HOH HOH . N 7 HOH A 50 350 5 HOH HOH . N 7 HOH A 51 351 217 HOH HOH . N 7 HOH A 52 352 129 HOH HOH . N 7 HOH A 53 353 99 HOH HOH . N 7 HOH A 54 354 38 HOH HOH . N 7 HOH A 55 355 62 HOH HOH . N 7 HOH A 56 356 123 HOH HOH . N 7 HOH A 57 357 160 HOH HOH . N 7 HOH A 58 358 13 HOH HOH . N 7 HOH A 59 359 55 HOH HOH . N 7 HOH A 60 360 108 HOH HOH . N 7 HOH A 61 361 78 HOH HOH . N 7 HOH A 62 362 216 HOH HOH . N 7 HOH A 63 363 40 HOH HOH . N 7 HOH A 64 364 213 HOH HOH . N 7 HOH A 65 365 47 HOH HOH . N 7 HOH A 66 366 12 HOH HOH . N 7 HOH A 67 367 176 HOH HOH . N 7 HOH A 68 368 67 HOH HOH . N 7 HOH A 69 369 196 HOH HOH . N 7 HOH A 70 370 194 HOH HOH . N 7 HOH A 71 371 136 HOH HOH . N 7 HOH A 72 372 87 HOH HOH . N 7 HOH A 73 373 170 HOH HOH . N 7 HOH A 74 374 172 HOH HOH . N 7 HOH A 75 375 53 HOH HOH . N 7 HOH A 76 376 118 HOH HOH . N 7 HOH A 77 377 101 HOH HOH . N 7 HOH A 78 378 6 HOH HOH . N 7 HOH A 79 379 80 HOH HOH . N 7 HOH A 80 380 233 HOH HOH . N 7 HOH A 81 381 229 HOH HOH . N 7 HOH A 82 382 174 HOH HOH . N 7 HOH A 83 383 124 HOH HOH . N 7 HOH A 84 384 34 HOH HOH . N 7 HOH A 85 385 211 HOH HOH . N 7 HOH A 86 386 57 HOH HOH . N 7 HOH A 87 387 133 HOH HOH . N 7 HOH A 88 388 14 HOH HOH . N 7 HOH A 89 389 59 HOH HOH . N 7 HOH A 90 390 68 HOH HOH . N 7 HOH A 91 391 164 HOH HOH . N 7 HOH A 92 392 97 HOH HOH . N 7 HOH A 93 393 221 HOH HOH . N 7 HOH A 94 394 162 HOH HOH . N 7 HOH A 95 395 152 HOH HOH . N 7 HOH A 96 396 93 HOH HOH . N 7 HOH A 97 397 98 HOH HOH . N 7 HOH A 98 398 139 HOH HOH . N 7 HOH A 99 399 54 HOH HOH . N 7 HOH A 100 400 218 HOH HOH . N 7 HOH A 101 401 188 HOH HOH . N 7 HOH A 102 402 235 HOH HOH . N 7 HOH A 103 403 206 HOH HOH . N 7 HOH A 104 404 71 HOH HOH . N 7 HOH A 105 405 110 HOH HOH . N 7 HOH A 106 406 195 HOH HOH . N 7 HOH A 107 407 126 HOH HOH . N 7 HOH A 108 408 113 HOH HOH . N 7 HOH A 109 409 65 HOH HOH . N 7 HOH A 110 410 159 HOH HOH . N 7 HOH A 111 411 186 HOH HOH . N 7 HOH A 112 412 184 HOH HOH . N 7 HOH A 113 413 85 HOH HOH . N 7 HOH A 114 414 189 HOH HOH . N 7 HOH A 115 415 96 HOH HOH . N 7 HOH A 116 416 190 HOH HOH . N 7 HOH A 117 417 185 HOH HOH . N 7 HOH A 118 418 208 HOH HOH . O 7 HOH B 1 301 224 HOH HOH . O 7 HOH B 2 302 114 HOH HOH . O 7 HOH B 3 303 128 HOH HOH . O 7 HOH B 4 304 63 HOH HOH . O 7 HOH B 5 305 167 HOH HOH . O 7 HOH B 6 306 115 HOH HOH . O 7 HOH B 7 307 48 HOH HOH . O 7 HOH B 8 308 121 HOH HOH . O 7 HOH B 9 309 138 HOH HOH . O 7 HOH B 10 310 31 HOH HOH . O 7 HOH B 11 311 3 HOH HOH . O 7 HOH B 12 312 222 HOH HOH . O 7 HOH B 13 313 39 HOH HOH . O 7 HOH B 14 314 94 HOH HOH . O 7 HOH B 15 315 165 HOH HOH . O 7 HOH B 16 316 20 HOH HOH . O 7 HOH B 17 317 227 HOH HOH . O 7 HOH B 18 318 4 HOH HOH . O 7 HOH B 19 319 237 HOH HOH . O 7 HOH B 20 320 130 HOH HOH . O 7 HOH B 21 321 70 HOH HOH . O 7 HOH B 22 322 61 HOH HOH . O 7 HOH B 23 323 151 HOH HOH . O 7 HOH B 24 324 155 HOH HOH . O 7 HOH B 25 325 84 HOH HOH . O 7 HOH B 26 326 192 HOH HOH . O 7 HOH B 27 327 106 HOH HOH . O 7 HOH B 28 328 44 HOH HOH . O 7 HOH B 29 329 10 HOH HOH . O 7 HOH B 30 330 104 HOH HOH . O 7 HOH B 31 331 122 HOH HOH . O 7 HOH B 32 332 117 HOH HOH . O 7 HOH B 33 333 19 HOH HOH . O 7 HOH B 34 334 116 HOH HOH . O 7 HOH B 35 335 25 HOH HOH . O 7 HOH B 36 336 173 HOH HOH . O 7 HOH B 37 337 147 HOH HOH . O 7 HOH B 38 338 219 HOH HOH . O 7 HOH B 39 339 111 HOH HOH . O 7 HOH B 40 340 81 HOH HOH . O 7 HOH B 41 341 24 HOH HOH . O 7 HOH B 42 342 17 HOH HOH . O 7 HOH B 43 343 169 HOH HOH . O 7 HOH B 44 344 89 HOH HOH . O 7 HOH B 45 345 72 HOH HOH . O 7 HOH B 46 346 37 HOH HOH . O 7 HOH B 47 347 23 HOH HOH . O 7 HOH B 48 348 145 HOH HOH . O 7 HOH B 49 349 234 HOH HOH . O 7 HOH B 50 350 107 HOH HOH . O 7 HOH B 51 351 175 HOH HOH . O 7 HOH B 52 352 33 HOH HOH . O 7 HOH B 53 353 18 HOH HOH . O 7 HOH B 54 354 102 HOH HOH . O 7 HOH B 55 355 103 HOH HOH . O 7 HOH B 56 356 137 HOH HOH . O 7 HOH B 57 357 86 HOH HOH . O 7 HOH B 58 358 95 HOH HOH . O 7 HOH B 59 359 79 HOH HOH . O 7 HOH B 60 360 28 HOH HOH . O 7 HOH B 61 361 163 HOH HOH . O 7 HOH B 62 362 56 HOH HOH . O 7 HOH B 63 363 49 HOH HOH . O 7 HOH B 64 364 109 HOH HOH . O 7 HOH B 65 365 161 HOH HOH . O 7 HOH B 66 366 15 HOH HOH . O 7 HOH B 67 367 225 HOH HOH . O 7 HOH B 68 368 158 HOH HOH . O 7 HOH B 69 369 92 HOH HOH . O 7 HOH B 70 370 202 HOH HOH . O 7 HOH B 71 371 30 HOH HOH . O 7 HOH B 72 372 8 HOH HOH . O 7 HOH B 73 373 203 HOH HOH . O 7 HOH B 74 374 64 HOH HOH . O 7 HOH B 75 375 105 HOH HOH . O 7 HOH B 76 376 26 HOH HOH . O 7 HOH B 77 377 83 HOH HOH . O 7 HOH B 78 378 200 HOH HOH . O 7 HOH B 79 379 197 HOH HOH . O 7 HOH B 80 380 45 HOH HOH . O 7 HOH B 81 381 201 HOH HOH . O 7 HOH B 82 382 74 HOH HOH . O 7 HOH B 83 383 150 HOH HOH . O 7 HOH B 84 384 182 HOH HOH . O 7 HOH B 85 385 220 HOH HOH . O 7 HOH B 86 386 88 HOH HOH . O 7 HOH B 87 387 100 HOH HOH . O 7 HOH B 88 388 46 HOH HOH . O 7 HOH B 89 389 43 HOH HOH . O 7 HOH B 90 390 142 HOH HOH . O 7 HOH B 91 391 119 HOH HOH . O 7 HOH B 92 392 50 HOH HOH . O 7 HOH B 93 393 76 HOH HOH . O 7 HOH B 94 394 120 HOH HOH . O 7 HOH B 95 395 178 HOH HOH . O 7 HOH B 96 396 131 HOH HOH . O 7 HOH B 97 397 205 HOH HOH . O 7 HOH B 98 398 226 HOH HOH . O 7 HOH B 99 399 198 HOH HOH . O 7 HOH B 100 400 204 HOH HOH . O 7 HOH B 101 401 135 HOH HOH . O 7 HOH B 102 402 199 HOH HOH . O 7 HOH B 103 403 127 HOH HOH . O 7 HOH B 104 404 223 HOH HOH . O 7 HOH B 105 405 191 HOH HOH . O 7 HOH B 106 406 51 HOH HOH . O 7 HOH B 107 407 132 HOH HOH . O 7 HOH B 108 408 215 HOH HOH . O 7 HOH B 109 409 193 HOH HOH . O 7 HOH B 110 410 183 HOH HOH . O 7 HOH B 111 411 141 HOH HOH . O 7 HOH B 112 412 148 HOH HOH . O 7 HOH B 113 413 149 HOH HOH . O 7 HOH B 114 414 210 HOH HOH . O 7 HOH B 115 415 58 HOH HOH . O 7 HOH B 116 416 140 HOH HOH . O 7 HOH B 117 417 207 HOH HOH . O 7 HOH B 118 418 187 HOH HOH . O 7 HOH B 119 419 209 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 29.815 _atom_site.Cartn_y 29.815 _atom_site.Cartn_z 0 _atom_site.occupancy 0.5 _atom_site.B_iso_or_equiv 30.28 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 202 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 1 #