data_3DX5 # _model_server_result.job_id sXp1RKE9zO0uCRBQTziKEg _model_server_result.datetime_utc '2024-11-27 23:17:19' _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 3dx5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":287}' # _entry.id 3DX5 # _exptl.entry_id 3DX5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (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 120 _cell.entry_id 3DX5 _cell.length_a 134.483 _cell.length_b 134.483 _cell.length_c 72.806 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DX5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # 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 dimeric 2 software_defined_assembly 1 ? monomeric 1 author_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 1,2 A,B,C,D,E,F,G 2 1 # 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' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 134.483 0 36.403 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A C MSE 1 A MSE 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C TYR 43 A TYR 43 1_555 A N MSE 44 A MSE 44 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C TYR 43 A TYR 43 1_555 A N MSE 44 A MSE 44 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C MSE 44 A MSE 44 1_555 A N GLN 45 A GLN 45 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C MSE 44 A MSE 44 1_555 A N GLN 45 A GLN 45 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C THR 65 A THR 65 1_555 A N MSE 66 A MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 A C MSE 66 A MSE 66 1_555 A N ILE 67 A ILE 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 A C ARG 126 A ARG 126 1_555 A N MSE 127 A MSE 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 A C MSE 127 A MSE 127 1_555 A N ILE 128 A ILE 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C ASN 136 A ASN 136 1_555 A N MSE 137 A MSE 137 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.324 ? covale ? covale11 A C ASN 136 A ASN 136 1_555 A N MSE 137 A MSE 137 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.327 ? covale ? covale12 A C MSE 137 A MSE 137 1_555 A N TYR 138 A TYR 138 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 A C MSE 137 A MSE 137 1_555 A N TYR 138 A TYR 138 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale14 A C GLY 225 A GLY 225 1_555 A N MSE 226 A MSE 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale15 A C MSE 226 A MSE 226 1_555 A N VAL 227 A VAL 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale16 A C GLU 266 A GLU 266 1_555 A N MSE 267 A MSE 267 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale17 A C GLU 266 A GLU 266 1_555 A N MSE 267 A MSE 267 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale18 A C MSE 267 A MSE 267 1_555 A N LYS 268 A LYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? metalc ? metalc1 A OE2 GLU 142 A GLU 142 1_555 B MN MN . A MN 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc2 A OD2 ASP 172 A ASP 172 1_555 B MN MN . A MN 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc3 A OE1 GLU 253 A GLU 253 1_555 B MN MN . A MN 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc4 A OE2 GLU 253 A GLU 253 1_555 B MN MN . A MN 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc5 B MN MN . A MN 287 1_555 D O3 DHB . A DHB 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3DX5 _atom_sites.fract_transf_matrix[1][1] 0.007436 _atom_sites.fract_transf_matrix[1][2] 0.004293 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008586 _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] 0.013735 _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 MN A 1 287 4 MN MN . C 3 CL A 1 288 5 CL CL . D 4 DHB A 1 289 1 DHB DHB . E 5 TRS A 1 290 3 TRS TRS . F 6 GOL A 1 291 2 GOL GOL . G 7 HOH A 1 292 1 HOH HOH . G 7 HOH A 2 293 2 HOH HOH . G 7 HOH A 3 294 3 HOH HOH . G 7 HOH A 4 295 4 HOH HOH . G 7 HOH A 5 296 5 HOH HOH . G 7 HOH A 6 297 6 HOH HOH . G 7 HOH A 7 298 7 HOH HOH . G 7 HOH A 8 299 8 HOH HOH . G 7 HOH A 9 300 9 HOH HOH . G 7 HOH A 10 301 10 HOH HOH . G 7 HOH A 11 302 11 HOH HOH . G 7 HOH A 12 303 12 HOH HOH . G 7 HOH A 13 304 13 HOH HOH . G 7 HOH A 14 305 14 HOH HOH . G 7 HOH A 15 306 15 HOH HOH . G 7 HOH A 16 307 16 HOH HOH . G 7 HOH A 17 308 17 HOH HOH . G 7 HOH A 18 309 18 HOH HOH . G 7 HOH A 19 310 19 HOH HOH . G 7 HOH A 20 311 20 HOH HOH . G 7 HOH A 21 312 21 HOH HOH . G 7 HOH A 22 313 22 HOH HOH . G 7 HOH A 23 314 23 HOH HOH . G 7 HOH A 24 315 24 HOH HOH . G 7 HOH A 25 316 25 HOH HOH . G 7 HOH A 26 317 26 HOH HOH . G 7 HOH A 27 318 27 HOH HOH . G 7 HOH A 28 319 28 HOH HOH . G 7 HOH A 29 320 29 HOH HOH . G 7 HOH A 30 321 30 HOH HOH . G 7 HOH A 31 322 31 HOH HOH . G 7 HOH A 32 323 32 HOH HOH . G 7 HOH A 33 324 33 HOH HOH . G 7 HOH A 34 325 34 HOH HOH . G 7 HOH A 35 326 35 HOH HOH . G 7 HOH A 36 327 36 HOH HOH . G 7 HOH A 37 328 37 HOH HOH . G 7 HOH A 38 329 38 HOH HOH . G 7 HOH A 39 330 39 HOH HOH . G 7 HOH A 40 331 40 HOH HOH . G 7 HOH A 41 332 41 HOH HOH . G 7 HOH A 42 333 42 HOH HOH . G 7 HOH A 43 334 43 HOH HOH . G 7 HOH A 44 335 44 HOH HOH . G 7 HOH A 45 336 45 HOH HOH . G 7 HOH A 46 337 46 HOH HOH . G 7 HOH A 47 338 47 HOH HOH . G 7 HOH A 48 339 48 HOH HOH . G 7 HOH A 49 340 49 HOH HOH . G 7 HOH A 50 341 50 HOH HOH . G 7 HOH A 51 342 51 HOH HOH . G 7 HOH A 52 343 52 HOH HOH . G 7 HOH A 53 344 53 HOH HOH . G 7 HOH A 54 345 54 HOH HOH . G 7 HOH A 55 346 55 HOH HOH . G 7 HOH A 56 347 56 HOH HOH . G 7 HOH A 57 348 57 HOH HOH . G 7 HOH A 58 349 58 HOH HOH . G 7 HOH A 59 350 59 HOH HOH . G 7 HOH A 60 351 60 HOH HOH . G 7 HOH A 61 352 61 HOH HOH . G 7 HOH A 62 353 62 HOH HOH . G 7 HOH A 63 354 63 HOH HOH . G 7 HOH A 64 355 64 HOH HOH . G 7 HOH A 65 356 65 HOH HOH . G 7 HOH A 66 357 66 HOH HOH . G 7 HOH A 67 358 67 HOH HOH . G 7 HOH A 68 359 68 HOH HOH . G 7 HOH A 69 360 69 HOH HOH . G 7 HOH A 70 361 70 HOH HOH . G 7 HOH A 71 362 71 HOH HOH . G 7 HOH A 72 363 72 HOH HOH . G 7 HOH A 73 364 73 HOH HOH . G 7 HOH A 74 365 74 HOH HOH . G 7 HOH A 75 366 75 HOH HOH . G 7 HOH A 76 367 76 HOH HOH . G 7 HOH A 77 368 77 HOH HOH . G 7 HOH A 78 369 78 HOH HOH . G 7 HOH A 79 370 79 HOH HOH . G 7 HOH A 80 371 80 HOH HOH . G 7 HOH A 81 372 81 HOH HOH . G 7 HOH A 82 373 82 HOH HOH . G 7 HOH A 83 374 83 HOH HOH . G 7 HOH A 84 375 84 HOH HOH . G 7 HOH A 85 376 85 HOH HOH . G 7 HOH A 86 377 86 HOH HOH . G 7 HOH A 87 378 87 HOH HOH . G 7 HOH A 88 379 88 HOH HOH . G 7 HOH A 89 380 89 HOH HOH . G 7 HOH A 90 381 90 HOH HOH . G 7 HOH A 91 382 91 HOH HOH . G 7 HOH A 92 383 92 HOH HOH . G 7 HOH A 93 384 93 HOH HOH . G 7 HOH A 94 385 94 HOH HOH . G 7 HOH A 95 386 95 HOH HOH . G 7 HOH A 96 387 96 HOH HOH . G 7 HOH A 97 388 97 HOH HOH . G 7 HOH A 98 389 98 HOH HOH . G 7 HOH A 99 390 99 HOH HOH . G 7 HOH A 100 391 100 HOH HOH . G 7 HOH A 101 392 101 HOH HOH . G 7 HOH A 102 393 102 HOH HOH . G 7 HOH A 103 394 103 HOH HOH . G 7 HOH A 104 395 104 HOH HOH . G 7 HOH A 105 396 105 HOH HOH . G 7 HOH A 106 397 106 HOH HOH . G 7 HOH A 107 398 107 HOH HOH . G 7 HOH A 108 399 108 HOH HOH . G 7 HOH A 109 400 109 HOH HOH . G 7 HOH A 110 401 110 HOH HOH . G 7 HOH A 111 402 111 HOH HOH . G 7 HOH A 112 403 112 HOH HOH . G 7 HOH A 113 404 113 HOH HOH . G 7 HOH A 114 405 114 HOH HOH . G 7 HOH A 115 406 115 HOH HOH . G 7 HOH A 116 407 116 HOH HOH . G 7 HOH A 117 408 117 HOH HOH . G 7 HOH A 118 409 118 HOH HOH . G 7 HOH A 119 410 119 HOH HOH . G 7 HOH A 120 411 120 HOH HOH . G 7 HOH A 121 412 121 HOH HOH . G 7 HOH A 122 413 122 HOH HOH . G 7 HOH A 123 414 123 HOH HOH . G 7 HOH A 124 415 124 HOH HOH . G 7 HOH A 125 416 125 HOH HOH . G 7 HOH A 126 417 126 HOH HOH . G 7 HOH A 127 418 127 HOH HOH . G 7 HOH A 128 419 128 HOH HOH . G 7 HOH A 129 420 129 HOH HOH . G 7 HOH A 130 421 130 HOH HOH . G 7 HOH A 131 422 131 HOH HOH . G 7 HOH A 132 423 132 HOH HOH . G 7 HOH A 133 424 133 HOH HOH . G 7 HOH A 134 425 134 HOH HOH . G 7 HOH A 135 426 135 HOH HOH . G 7 HOH A 136 427 136 HOH HOH . G 7 HOH A 137 428 137 HOH HOH . G 7 HOH A 138 429 138 HOH HOH . G 7 HOH A 139 430 139 HOH HOH . G 7 HOH A 140 431 140 HOH HOH . G 7 HOH A 141 432 141 HOH HOH . G 7 HOH A 142 433 142 HOH HOH . G 7 HOH A 143 434 143 HOH HOH . G 7 HOH A 144 435 144 HOH HOH . G 7 HOH A 145 436 145 HOH HOH . G 7 HOH A 146 437 146 HOH HOH . G 7 HOH A 147 438 147 HOH HOH . G 7 HOH A 148 439 148 HOH HOH . G 7 HOH A 149 440 149 HOH HOH . G 7 HOH A 150 441 150 HOH HOH . G 7 HOH A 151 442 151 HOH HOH . G 7 HOH A 152 443 152 HOH HOH . G 7 HOH A 153 444 153 HOH HOH . G 7 HOH A 154 445 154 HOH HOH . G 7 HOH A 155 446 155 HOH HOH . G 7 HOH A 156 447 156 HOH HOH . G 7 HOH A 157 448 157 HOH HOH . G 7 HOH A 158 449 158 HOH HOH . G 7 HOH A 159 450 159 HOH HOH . G 7 HOH A 160 451 160 HOH HOH . G 7 HOH A 161 452 161 HOH HOH . G 7 HOH A 162 453 162 HOH HOH . G 7 HOH A 163 454 163 HOH HOH . G 7 HOH A 164 455 164 HOH HOH . G 7 HOH A 165 456 165 HOH HOH . G 7 HOH A 166 457 166 HOH HOH . G 7 HOH A 167 458 167 HOH HOH . G 7 HOH A 168 459 168 HOH HOH . G 7 HOH A 169 460 169 HOH HOH . G 7 HOH A 170 461 170 HOH HOH . G 7 HOH A 171 462 171 HOH HOH . G 7 HOH A 172 463 172 HOH HOH . G 7 HOH A 173 464 173 HOH HOH . G 7 HOH A 174 465 174 HOH HOH . G 7 HOH A 175 466 175 HOH HOH . G 7 HOH A 176 467 176 HOH HOH . G 7 HOH A 177 468 177 HOH HOH . G 7 HOH A 178 469 178 HOH HOH . G 7 HOH A 179 470 179 HOH HOH . G 7 HOH A 180 471 180 HOH HOH . G 7 HOH A 181 472 181 HOH HOH . G 7 HOH A 182 473 182 HOH HOH . G 7 HOH A 183 474 183 HOH HOH . G 7 HOH A 184 475 184 HOH HOH . G 7 HOH A 185 476 185 HOH HOH . G 7 HOH A 186 477 186 HOH HOH . G 7 HOH A 187 478 187 HOH HOH . G 7 HOH A 188 479 188 HOH HOH . G 7 HOH A 189 480 189 HOH HOH . G 7 HOH A 190 481 190 HOH HOH . G 7 HOH A 191 482 191 HOH HOH . G 7 HOH A 192 483 192 HOH HOH . G 7 HOH A 193 484 193 HOH HOH . G 7 HOH A 194 485 194 HOH HOH . G 7 HOH A 195 486 195 HOH HOH . G 7 HOH A 196 487 196 HOH HOH . G 7 HOH A 197 488 197 HOH HOH . G 7 HOH A 198 489 198 HOH HOH . G 7 HOH A 199 490 199 HOH HOH . G 7 HOH A 200 491 200 HOH HOH . G 7 HOH A 201 492 201 HOH HOH . G 7 HOH A 202 493 202 HOH HOH . G 7 HOH A 203 494 203 HOH HOH . G 7 HOH A 204 495 204 HOH HOH . G 7 HOH A 205 496 205 HOH HOH . G 7 HOH A 206 497 206 HOH HOH . G 7 HOH A 207 498 207 HOH HOH . G 7 HOH A 208 499 208 HOH HOH . G 7 HOH A 209 500 209 HOH HOH . G 7 HOH A 210 501 210 HOH HOH . G 7 HOH A 211 502 211 HOH HOH . G 7 HOH A 212 503 212 HOH HOH . G 7 HOH A 213 504 213 HOH HOH . G 7 HOH A 214 505 214 HOH HOH . G 7 HOH A 215 506 215 HOH HOH . G 7 HOH A 216 507 216 HOH HOH . G 7 HOH A 217 508 217 HOH HOH . G 7 HOH A 218 509 218 HOH HOH . G 7 HOH A 219 510 219 HOH HOH . G 7 HOH A 220 511 220 HOH HOH . G 7 HOH A 221 512 221 HOH HOH . G 7 HOH A 222 513 222 HOH HOH . G 7 HOH A 223 514 223 HOH HOH . G 7 HOH A 224 515 224 HOH HOH . G 7 HOH A 225 516 225 HOH HOH . G 7 HOH A 226 517 226 HOH HOH . G 7 HOH A 227 518 227 HOH HOH . G 7 HOH A 228 519 228 HOH HOH . G 7 HOH A 229 520 229 HOH HOH . G 7 HOH A 230 521 230 HOH HOH . G 7 HOH A 231 522 231 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id B _atom_site.label_entity_id 2 _atom_site.Cartn_x 69.286 _atom_site.Cartn_y 67.179 _atom_site.Cartn_z 3.291 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 13.95 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 287 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #