data_3B2Y # _model_server_result.job_id AzjB6QTSS2yRodtzEv1zOQ _model_server_result.datetime_utc '2024-11-13 07:14:50' _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 3b2y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":275}' # _entry.id 3B2Y # _exptl.entry_id 3B2Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 2 _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 116.28 _cell.angle_gamma 90 _cell.entry_id 3B2Y _cell.length_a 43.715 _cell.length_b 127.577 _cell.length_c 49.303 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B2Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,E 1 1 B,D,F 2 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 ? 2 C N N ? 2 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 covale ? covale1 A C MSE 2 A MSE 1 1_555 A N THR 3 A THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C GLY 85 A GLY 84 1_555 A N MSE 86 A MSE 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C MSE 86 A MSE 85 1_555 A N LEU 87 A LEU 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale4 A C LEU 174 A LEU 173 1_555 A N MSE 175 A MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale5 A C MSE 175 A MSE 174 1_555 A N ASN 176 A ASN 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale6 A C ALA 263 A ALA 262 1_555 A N MSE 264 A MSE 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C MSE 264 A MSE 263 1_555 A N GLY 265 A GLY 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 B C MSE 2 B MSE 1 1_555 B N THR 3 B THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 B C GLY 85 B GLY 84 1_555 B N MSE 86 B MSE 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale10 B C MSE 86 B MSE 85 1_555 B N LEU 87 B LEU 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale11 B C LEU 174 B LEU 173 1_555 B N MSE 175 B MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale12 B C MSE 175 B MSE 174 1_555 B N ASN 176 B ASN 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 B C ALA 263 B ALA 262 1_555 B N MSE 264 B MSE 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale14 B C MSE 264 B MSE 263 1_555 B N GLY 265 B GLY 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? metalc ? metalc1 A ND1 HIS 76 A HIS 75 1_555 C NI NI . A NI 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc2 A OE1 GLU 79 A GLU 78 1_555 C NI NI . A NI 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc3 A OE2 GLU 79 A GLU 78 1_555 C NI NI . A NI 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc4 A ND1 HIS 170 A HIS 169 1_555 C NI NI . A NI 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc5 C NI NI . A NI 275 1_555 E O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc6 C NI NI . A NI 275 1_555 E O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc7 B ND1 HIS 76 B HIS 75 1_555 D NI NI . B NI 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc8 B OE1 GLU 79 B GLU 78 1_555 D NI NI . B NI 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc9 B OE2 GLU 79 B GLU 78 1_555 D NI NI . B NI 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc10 B ND1 HIS 170 B HIS 169 1_555 D NI NI . B NI 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc11 D NI NI . B NI 275 1_555 F O HOH . B HOH 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? # _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 3B2Y _atom_sites.fract_transf_matrix[1][1] 0.022875 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.011294 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007838 _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] 0.02262 _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 NI A 1 275 1 NI NI . D 2 NI B 1 275 2 NI NI . E 3 HOH A 1 276 3 HOH HOH . E 3 HOH A 2 277 6 HOH HOH . E 3 HOH A 3 278 7 HOH HOH . E 3 HOH A 4 279 8 HOH HOH . E 3 HOH A 5 280 10 HOH HOH . E 3 HOH A 6 281 16 HOH HOH . E 3 HOH A 7 282 18 HOH HOH . E 3 HOH A 8 283 19 HOH HOH . E 3 HOH A 9 284 22 HOH HOH . E 3 HOH A 10 285 23 HOH HOH . E 3 HOH A 11 286 24 HOH HOH . E 3 HOH A 12 287 25 HOH HOH . E 3 HOH A 13 288 27 HOH HOH . E 3 HOH A 14 289 28 HOH HOH . E 3 HOH A 15 290 32 HOH HOH . E 3 HOH A 16 291 33 HOH HOH . E 3 HOH A 17 292 34 HOH HOH . E 3 HOH A 18 293 35 HOH HOH . E 3 HOH A 19 294 38 HOH HOH . E 3 HOH A 20 295 39 HOH HOH . E 3 HOH A 21 296 42 HOH HOH . E 3 HOH A 22 297 44 HOH HOH . E 3 HOH A 23 298 47 HOH HOH . E 3 HOH A 24 299 49 HOH HOH . E 3 HOH A 25 300 50 HOH HOH . E 3 HOH A 26 301 54 HOH HOH . E 3 HOH A 27 302 55 HOH HOH . E 3 HOH A 28 303 56 HOH HOH . E 3 HOH A 29 304 57 HOH HOH . E 3 HOH A 30 305 59 HOH HOH . E 3 HOH A 31 306 63 HOH HOH . E 3 HOH A 32 307 64 HOH HOH . E 3 HOH A 33 308 66 HOH HOH . E 3 HOH A 34 309 68 HOH HOH . E 3 HOH A 35 310 71 HOH HOH . E 3 HOH A 36 311 73 HOH HOH . E 3 HOH A 37 312 75 HOH HOH . E 3 HOH A 38 313 78 HOH HOH . E 3 HOH A 39 314 81 HOH HOH . E 3 HOH A 40 315 82 HOH HOH . E 3 HOH A 41 316 87 HOH HOH . E 3 HOH A 42 317 89 HOH HOH . E 3 HOH A 43 318 90 HOH HOH . E 3 HOH A 44 319 91 HOH HOH . E 3 HOH A 45 320 92 HOH HOH . E 3 HOH A 46 321 93 HOH HOH . E 3 HOH A 47 322 94 HOH HOH . E 3 HOH A 48 323 95 HOH HOH . E 3 HOH A 49 324 97 HOH HOH . E 3 HOH A 50 325 98 HOH HOH . E 3 HOH A 51 326 104 HOH HOH . E 3 HOH A 52 327 109 HOH HOH . E 3 HOH A 53 328 110 HOH HOH . E 3 HOH A 54 329 115 HOH HOH . E 3 HOH A 55 330 116 HOH HOH . E 3 HOH A 56 331 117 HOH HOH . E 3 HOH A 57 332 118 HOH HOH . E 3 HOH A 58 333 121 HOH HOH . E 3 HOH A 59 334 123 HOH HOH . E 3 HOH A 60 335 127 HOH HOH . E 3 HOH A 61 336 129 HOH HOH . E 3 HOH A 62 337 130 HOH HOH . E 3 HOH A 63 338 132 HOH HOH . E 3 HOH A 64 339 133 HOH HOH . E 3 HOH A 65 340 136 HOH HOH . E 3 HOH A 66 341 137 HOH HOH . E 3 HOH A 67 342 139 HOH HOH . E 3 HOH A 68 343 141 HOH HOH . E 3 HOH A 69 344 142 HOH HOH . E 3 HOH A 70 345 144 HOH HOH . E 3 HOH A 71 346 147 HOH HOH . E 3 HOH A 72 347 148 HOH HOH . E 3 HOH A 73 348 150 HOH HOH . E 3 HOH A 74 349 151 HOH HOH . E 3 HOH A 75 350 153 HOH HOH . E 3 HOH A 76 351 154 HOH HOH . E 3 HOH A 77 352 156 HOH HOH . E 3 HOH A 78 353 157 HOH HOH . E 3 HOH A 79 354 159 HOH HOH . E 3 HOH A 80 355 160 HOH HOH . E 3 HOH A 81 356 162 HOH HOH . E 3 HOH A 82 357 163 HOH HOH . E 3 HOH A 83 358 165 HOH HOH . E 3 HOH A 84 359 167 HOH HOH . E 3 HOH A 85 360 168 HOH HOH . E 3 HOH A 86 361 169 HOH HOH . E 3 HOH A 87 362 171 HOH HOH . E 3 HOH A 88 363 172 HOH HOH . E 3 HOH A 89 364 173 HOH HOH . E 3 HOH A 90 365 174 HOH HOH . E 3 HOH A 91 366 176 HOH HOH . E 3 HOH A 92 367 177 HOH HOH . E 3 HOH A 93 368 178 HOH HOH . E 3 HOH A 94 369 179 HOH HOH . E 3 HOH A 95 370 180 HOH HOH . E 3 HOH A 96 371 182 HOH HOH . E 3 HOH A 97 372 183 HOH HOH . E 3 HOH A 98 373 184 HOH HOH . E 3 HOH A 99 374 189 HOH HOH . E 3 HOH A 100 375 190 HOH HOH . E 3 HOH A 101 376 191 HOH HOH . E 3 HOH A 102 377 193 HOH HOH . E 3 HOH A 103 378 194 HOH HOH . E 3 HOH A 104 379 198 HOH HOH . E 3 HOH A 105 380 200 HOH HOH . E 3 HOH A 106 381 201 HOH HOH . E 3 HOH A 107 382 202 HOH HOH . E 3 HOH A 108 383 203 HOH HOH . E 3 HOH A 109 384 205 HOH HOH . E 3 HOH A 110 385 206 HOH HOH . E 3 HOH A 111 386 208 HOH HOH . E 3 HOH A 112 387 209 HOH HOH . E 3 HOH A 113 388 210 HOH HOH . E 3 HOH A 114 389 211 HOH HOH . E 3 HOH A 115 390 212 HOH HOH . E 3 HOH A 116 391 213 HOH HOH . E 3 HOH A 117 392 216 HOH HOH . E 3 HOH A 118 393 217 HOH HOH . E 3 HOH A 119 394 220 HOH HOH . E 3 HOH A 120 395 222 HOH HOH . E 3 HOH A 121 396 224 HOH HOH . E 3 HOH A 122 397 227 HOH HOH . E 3 HOH A 123 398 229 HOH HOH . E 3 HOH A 124 399 232 HOH HOH . F 3 HOH B 1 276 4 HOH HOH . F 3 HOH B 2 277 5 HOH HOH . F 3 HOH B 3 278 9 HOH HOH . F 3 HOH B 4 279 11 HOH HOH . F 3 HOH B 5 280 12 HOH HOH . F 3 HOH B 6 281 13 HOH HOH . F 3 HOH B 7 282 14 HOH HOH . F 3 HOH B 8 283 15 HOH HOH . F 3 HOH B 9 284 17 HOH HOH . F 3 HOH B 10 285 20 HOH HOH . F 3 HOH B 11 286 21 HOH HOH . F 3 HOH B 12 287 26 HOH HOH . F 3 HOH B 13 288 29 HOH HOH . F 3 HOH B 14 289 30 HOH HOH . F 3 HOH B 15 290 31 HOH HOH . F 3 HOH B 16 291 36 HOH HOH . F 3 HOH B 17 292 37 HOH HOH . F 3 HOH B 18 293 40 HOH HOH . F 3 HOH B 19 294 41 HOH HOH . F 3 HOH B 20 295 43 HOH HOH . F 3 HOH B 21 296 45 HOH HOH . F 3 HOH B 22 297 46 HOH HOH . F 3 HOH B 23 298 48 HOH HOH . F 3 HOH B 24 299 51 HOH HOH . F 3 HOH B 25 300 52 HOH HOH . F 3 HOH B 26 301 53 HOH HOH . F 3 HOH B 27 302 58 HOH HOH . F 3 HOH B 28 303 60 HOH HOH . F 3 HOH B 29 304 61 HOH HOH . F 3 HOH B 30 305 62 HOH HOH . F 3 HOH B 31 306 65 HOH HOH . F 3 HOH B 32 307 67 HOH HOH . F 3 HOH B 33 308 69 HOH HOH . F 3 HOH B 34 309 70 HOH HOH . F 3 HOH B 35 310 72 HOH HOH . F 3 HOH B 36 311 74 HOH HOH . F 3 HOH B 37 312 76 HOH HOH . F 3 HOH B 38 313 77 HOH HOH . F 3 HOH B 39 314 79 HOH HOH . F 3 HOH B 40 315 80 HOH HOH . F 3 HOH B 41 316 83 HOH HOH . F 3 HOH B 42 317 84 HOH HOH . F 3 HOH B 43 318 85 HOH HOH . F 3 HOH B 44 319 86 HOH HOH . F 3 HOH B 45 320 88 HOH HOH . F 3 HOH B 46 321 96 HOH HOH . F 3 HOH B 47 322 99 HOH HOH . F 3 HOH B 48 323 100 HOH HOH . F 3 HOH B 49 324 101 HOH HOH . F 3 HOH B 50 325 102 HOH HOH . F 3 HOH B 51 326 103 HOH HOH . F 3 HOH B 52 327 105 HOH HOH . F 3 HOH B 53 328 106 HOH HOH . F 3 HOH B 54 329 107 HOH HOH . F 3 HOH B 55 330 108 HOH HOH . F 3 HOH B 56 331 111 HOH HOH . F 3 HOH B 57 332 112 HOH HOH . F 3 HOH B 58 333 113 HOH HOH . F 3 HOH B 59 334 114 HOH HOH . F 3 HOH B 60 335 119 HOH HOH . F 3 HOH B 61 336 120 HOH HOH . F 3 HOH B 62 337 122 HOH HOH . F 3 HOH B 63 338 124 HOH HOH . F 3 HOH B 64 339 125 HOH HOH . F 3 HOH B 65 340 126 HOH HOH . F 3 HOH B 66 341 128 HOH HOH . F 3 HOH B 67 342 131 HOH HOH . F 3 HOH B 68 343 134 HOH HOH . F 3 HOH B 69 344 135 HOH HOH . F 3 HOH B 70 345 138 HOH HOH . F 3 HOH B 71 346 140 HOH HOH . F 3 HOH B 72 347 143 HOH HOH . F 3 HOH B 73 348 145 HOH HOH . F 3 HOH B 74 349 146 HOH HOH . F 3 HOH B 75 350 149 HOH HOH . F 3 HOH B 76 351 152 HOH HOH . F 3 HOH B 77 352 155 HOH HOH . F 3 HOH B 78 353 158 HOH HOH . F 3 HOH B 79 354 161 HOH HOH . F 3 HOH B 80 355 164 HOH HOH . F 3 HOH B 81 356 166 HOH HOH . F 3 HOH B 82 357 170 HOH HOH . F 3 HOH B 83 358 175 HOH HOH . F 3 HOH B 84 359 181 HOH HOH . F 3 HOH B 85 360 185 HOH HOH . F 3 HOH B 86 361 186 HOH HOH . F 3 HOH B 87 362 187 HOH HOH . F 3 HOH B 88 363 188 HOH HOH . F 3 HOH B 89 364 192 HOH HOH . F 3 HOH B 90 365 195 HOH HOH . F 3 HOH B 91 366 196 HOH HOH . F 3 HOH B 92 367 197 HOH HOH . F 3 HOH B 93 368 199 HOH HOH . F 3 HOH B 94 369 204 HOH HOH . F 3 HOH B 95 370 207 HOH HOH . F 3 HOH B 96 371 214 HOH HOH . F 3 HOH B 97 372 215 HOH HOH . F 3 HOH B 98 373 218 HOH HOH . F 3 HOH B 99 374 219 HOH HOH . F 3 HOH B 100 375 221 HOH HOH . F 3 HOH B 101 376 223 HOH HOH . F 3 HOH B 102 377 225 HOH HOH . F 3 HOH B 103 378 226 HOH HOH . F 3 HOH B 104 379 228 HOH HOH . F 3 HOH B 105 380 230 HOH HOH . F 3 HOH B 106 381 231 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 2 _atom_site.Cartn_x 20.438 _atom_site.Cartn_y 49.97 _atom_site.Cartn_z 60.217 _atom_site.occupancy 0.7 _atom_site.B_iso_or_equiv 29.4 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 275 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #