data_5VXA # _model_server_result.job_id YpVLGBVJkZDInMhFGpewGA _model_server_result.datetime_utc '2024-12-13 13:43:27' _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 5vxa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":206}' # _entry.id 5VXA # _exptl.entry_id 5VXA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM 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 5VXA _cell.length_a 47.78 _cell.length_b 80.37 _cell.length_c 114.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VXA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,N 1 1 B,I,J,K,L,M,O 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 3 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 6 _struct_asym.id H _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 SG CYS 134 A CYS 133 1_555 G S2 BME . A BME 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? covale ? covale2 B SG CYS 134 B CYS 133 1_555 L S2 BME . B BME 204 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.102 ? covale ? covale3 B SG CYS 134 B CYS 133 1_555 L S2 BME . B BME 204 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.081 ? metalc ? metalc1 A NE2 HIS 36 A HIS 35 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc2 A NE2 HIS 62 A HIS 61 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc3 A OD2 ASP 63 A ASP 62 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc4 A OD1 ASP 123 A ASP 122 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc5 C ZN ZN . A ZN 201 1_555 N O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc6 D O2A NDP . A NDP 202 1_555 H NA NA . A NA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc7 D O1N NDP . A NDP 202 1_555 H NA NA . A NA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc8 B NE2 HIS 36 B HIS 35 1_555 I ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc9 B NE2 HIS 62 B HIS 61 1_555 I ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc10 B OD2 ASP 63 B ASP 62 1_555 I ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc11 B OD1 ASP 123 B ASP 122 1_555 I ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc12 I ZN ZN . B ZN 201 1_555 O O HOH . B HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5VXA _atom_sites.fract_transf_matrix[1][1] 0.020929 _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] 0.012442 _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] 0.008737 _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 ZN A 1 201 199 ZN ZN . D 3 NDP A 1 202 1 NDP NDP . E 4 EDO A 1 203 2 EDO EDO . F 4 EDO A 1 204 3 EDO EDO . G 5 BME A 1 205 2 BME BME . H 6 NA A 1 206 1 NA NA . I 2 ZN B 1 201 199 ZN ZN . J 3 NDP B 1 202 1 NDP NDP . K 4 EDO B 1 203 1 EDO EDO . L 5 BME B 1 204 1 BME BME . M 7 TRS B 1 205 1 TRS TRS . N 8 HOH A 1 301 216 HOH HOH . N 8 HOH A 2 302 42 HOH HOH . N 8 HOH A 3 303 194 HOH HOH . N 8 HOH A 4 304 164 HOH HOH . N 8 HOH A 5 305 140 HOH HOH . N 8 HOH A 6 306 175 HOH HOH . N 8 HOH A 7 307 190 HOH HOH . N 8 HOH A 8 308 155 HOH HOH . N 8 HOH A 9 309 227 HOH HOH . N 8 HOH A 10 310 75 HOH HOH . N 8 HOH A 11 311 102 HOH HOH . N 8 HOH A 12 312 82 HOH HOH . N 8 HOH A 13 313 184 HOH HOH . N 8 HOH A 14 314 191 HOH HOH . N 8 HOH A 15 315 253 HOH HOH . N 8 HOH A 16 316 56 HOH HOH . N 8 HOH A 17 317 183 HOH HOH . N 8 HOH A 18 318 174 HOH HOH . N 8 HOH A 19 319 159 HOH HOH . N 8 HOH A 20 320 45 HOH HOH . N 8 HOH A 21 321 91 HOH HOH . N 8 HOH A 22 322 47 HOH HOH . N 8 HOH A 23 323 58 HOH HOH . N 8 HOH A 24 324 126 HOH HOH . N 8 HOH A 25 325 34 HOH HOH . N 8 HOH A 26 326 93 HOH HOH . N 8 HOH A 27 327 148 HOH HOH . N 8 HOH A 28 328 120 HOH HOH . N 8 HOH A 29 329 109 HOH HOH . N 8 HOH A 30 330 218 HOH HOH . N 8 HOH A 31 331 52 HOH HOH . N 8 HOH A 32 332 11 HOH HOH . N 8 HOH A 33 333 3 HOH HOH . N 8 HOH A 34 334 228 HOH HOH . N 8 HOH A 35 335 33 HOH HOH . N 8 HOH A 36 336 221 HOH HOH . N 8 HOH A 37 337 29 HOH HOH . N 8 HOH A 38 338 6 HOH HOH . N 8 HOH A 39 339 192 HOH HOH . N 8 HOH A 40 340 141 HOH HOH . N 8 HOH A 41 341 107 HOH HOH . N 8 HOH A 42 342 223 HOH HOH . N 8 HOH A 43 343 98 HOH HOH . N 8 HOH A 44 344 43 HOH HOH . N 8 HOH A 45 345 133 HOH HOH . N 8 HOH A 46 346 62 HOH HOH . N 8 HOH A 47 347 165 HOH HOH . N 8 HOH A 48 348 193 HOH HOH . N 8 HOH A 49 349 252 HOH HOH . N 8 HOH A 50 350 220 HOH HOH . N 8 HOH A 51 351 125 HOH HOH . N 8 HOH A 52 352 60 HOH HOH . N 8 HOH A 53 353 70 HOH HOH . N 8 HOH A 54 354 161 HOH HOH . N 8 HOH A 55 355 180 HOH HOH . N 8 HOH A 56 356 173 HOH HOH . N 8 HOH A 57 357 247 HOH HOH . N 8 HOH A 58 358 50 HOH HOH . N 8 HOH A 59 359 54 HOH HOH . N 8 HOH A 60 360 65 HOH HOH . N 8 HOH A 61 361 222 HOH HOH . N 8 HOH A 62 362 142 HOH HOH . N 8 HOH A 63 363 67 HOH HOH . N 8 HOH A 64 364 134 HOH HOH . N 8 HOH A 65 365 2 HOH HOH . N 8 HOH A 66 366 18 HOH HOH . N 8 HOH A 67 367 136 HOH HOH . N 8 HOH A 68 368 28 HOH HOH . N 8 HOH A 69 369 106 HOH HOH . N 8 HOH A 70 370 79 HOH HOH . N 8 HOH A 71 371 240 HOH HOH . N 8 HOH A 72 372 87 HOH HOH . N 8 HOH A 73 373 38 HOH HOH . N 8 HOH A 74 374 111 HOH HOH . N 8 HOH A 75 375 99 HOH HOH . N 8 HOH A 76 376 162 HOH HOH . N 8 HOH A 77 377 16 HOH HOH . N 8 HOH A 78 378 128 HOH HOH . N 8 HOH A 79 379 217 HOH HOH . N 8 HOH A 80 380 246 HOH HOH . N 8 HOH A 81 381 248 HOH HOH . N 8 HOH A 82 382 57 HOH HOH . N 8 HOH A 83 383 239 HOH HOH . N 8 HOH A 84 384 104 HOH HOH . N 8 HOH A 85 385 110 HOH HOH . N 8 HOH A 86 386 170 HOH HOH . N 8 HOH A 87 387 74 HOH HOH . N 8 HOH A 88 388 156 HOH HOH . N 8 HOH A 89 389 154 HOH HOH . N 8 HOH A 90 390 182 HOH HOH . N 8 HOH A 91 391 181 HOH HOH . N 8 HOH A 92 392 249 HOH HOH . N 8 HOH A 93 393 17 HOH HOH . N 8 HOH A 94 394 219 HOH HOH . N 8 HOH A 95 395 244 HOH HOH . N 8 HOH A 96 396 243 HOH HOH . N 8 HOH A 97 397 226 HOH HOH . N 8 HOH A 98 398 225 HOH HOH . N 8 HOH A 99 399 44 HOH HOH . N 8 HOH A 100 400 149 HOH HOH . O 8 HOH B 1 301 201 HOH HOH . O 8 HOH B 2 302 117 HOH HOH . O 8 HOH B 3 303 242 HOH HOH . O 8 HOH B 4 304 171 HOH HOH . O 8 HOH B 5 305 204 HOH HOH . O 8 HOH B 6 306 230 HOH HOH . O 8 HOH B 7 307 245 HOH HOH . O 8 HOH B 8 308 202 HOH HOH . O 8 HOH B 9 309 213 HOH HOH . O 8 HOH B 10 310 207 HOH HOH . O 8 HOH B 11 311 73 HOH HOH . O 8 HOH B 12 312 189 HOH HOH . O 8 HOH B 13 313 137 HOH HOH . O 8 HOH B 14 314 36 HOH HOH . O 8 HOH B 15 315 168 HOH HOH . O 8 HOH B 16 316 187 HOH HOH . O 8 HOH B 17 317 186 HOH HOH . O 8 HOH B 18 318 90 HOH HOH . O 8 HOH B 19 319 66 HOH HOH . O 8 HOH B 20 320 22 HOH HOH . O 8 HOH B 21 321 46 HOH HOH . O 8 HOH B 22 322 7 HOH HOH . O 8 HOH B 23 323 198 HOH HOH . O 8 HOH B 24 324 48 HOH HOH . O 8 HOH B 25 325 211 HOH HOH . O 8 HOH B 26 326 10 HOH HOH . O 8 HOH B 27 327 94 HOH HOH . O 8 HOH B 28 328 241 HOH HOH . O 8 HOH B 29 329 41 HOH HOH . O 8 HOH B 30 330 103 HOH HOH . O 8 HOH B 31 331 24 HOH HOH . O 8 HOH B 32 332 31 HOH HOH . O 8 HOH B 33 333 112 HOH HOH . O 8 HOH B 34 334 229 HOH HOH . O 8 HOH B 35 335 151 HOH HOH . O 8 HOH B 36 336 5 HOH HOH . O 8 HOH B 37 337 138 HOH HOH . O 8 HOH B 38 338 123 HOH HOH . O 8 HOH B 39 339 124 HOH HOH . O 8 HOH B 40 340 15 HOH HOH . O 8 HOH B 41 341 215 HOH HOH . O 8 HOH B 42 342 97 HOH HOH . O 8 HOH B 43 343 92 HOH HOH . O 8 HOH B 44 344 114 HOH HOH . O 8 HOH B 45 345 9 HOH HOH . O 8 HOH B 46 346 130 HOH HOH . O 8 HOH B 47 347 59 HOH HOH . O 8 HOH B 48 348 234 HOH HOH . O 8 HOH B 49 349 21 HOH HOH . O 8 HOH B 50 350 26 HOH HOH . O 8 HOH B 51 351 37 HOH HOH . O 8 HOH B 52 352 64 HOH HOH . O 8 HOH B 53 353 19 HOH HOH . O 8 HOH B 54 354 146 HOH HOH . O 8 HOH B 55 355 8 HOH HOH . O 8 HOH B 56 356 4 HOH HOH . O 8 HOH B 57 357 96 HOH HOH . O 8 HOH B 58 358 147 HOH HOH . O 8 HOH B 59 359 209 HOH HOH . O 8 HOH B 60 360 32 HOH HOH . O 8 HOH B 61 361 88 HOH HOH . O 8 HOH B 62 362 49 HOH HOH . O 8 HOH B 63 363 135 HOH HOH . O 8 HOH B 64 364 122 HOH HOH . O 8 HOH B 65 365 95 HOH HOH . O 8 HOH B 66 366 115 HOH HOH . O 8 HOH B 67 367 14 HOH HOH . O 8 HOH B 68 368 210 HOH HOH . O 8 HOH B 69 369 35 HOH HOH . O 8 HOH B 70 370 119 HOH HOH . O 8 HOH B 71 371 53 HOH HOH . O 8 HOH B 72 372 83 HOH HOH . O 8 HOH B 73 373 13 HOH HOH . O 8 HOH B 74 374 185 HOH HOH . O 8 HOH B 75 375 23 HOH HOH . O 8 HOH B 76 376 30 HOH HOH . O 8 HOH B 77 377 27 HOH HOH . O 8 HOH B 78 378 77 HOH HOH . O 8 HOH B 79 379 256 HOH HOH . O 8 HOH B 80 380 89 HOH HOH . O 8 HOH B 81 381 152 HOH HOH . O 8 HOH B 82 382 113 HOH HOH . O 8 HOH B 83 383 85 HOH HOH . O 8 HOH B 84 384 214 HOH HOH . O 8 HOH B 85 385 55 HOH HOH . O 8 HOH B 86 386 238 HOH HOH . O 8 HOH B 87 387 1 HOH HOH . O 8 HOH B 88 388 116 HOH HOH . O 8 HOH B 89 389 231 HOH HOH . O 8 HOH B 90 390 76 HOH HOH . O 8 HOH B 91 391 40 HOH HOH . O 8 HOH B 92 392 145 HOH HOH . O 8 HOH B 93 393 188 HOH HOH . O 8 HOH B 94 394 121 HOH HOH . O 8 HOH B 95 395 81 HOH HOH . O 8 HOH B 96 396 129 HOH HOH . O 8 HOH B 97 397 80 HOH HOH . O 8 HOH B 98 398 68 HOH HOH . O 8 HOH B 99 399 69 HOH HOH . O 8 HOH B 100 400 169 HOH HOH . O 8 HOH B 101 401 108 HOH HOH . O 8 HOH B 102 402 84 HOH HOH . O 8 HOH B 103 403 199 HOH HOH . O 8 HOH B 104 404 206 HOH HOH . O 8 HOH B 105 405 195 HOH HOH . O 8 HOH B 106 406 25 HOH HOH . O 8 HOH B 107 407 196 HOH HOH . O 8 HOH B 108 408 150 HOH HOH . O 8 HOH B 109 409 12 HOH HOH . O 8 HOH B 110 410 86 HOH HOH . O 8 HOH B 111 411 100 HOH HOH . O 8 HOH B 112 412 61 HOH HOH . O 8 HOH B 113 413 105 HOH HOH . O 8 HOH B 114 414 20 HOH HOH . O 8 HOH B 115 415 153 HOH HOH . O 8 HOH B 116 416 178 HOH HOH . O 8 HOH B 117 417 172 HOH HOH . O 8 HOH B 118 418 63 HOH HOH . O 8 HOH B 119 419 208 HOH HOH . O 8 HOH B 120 420 39 HOH HOH . O 8 HOH B 121 421 179 HOH HOH . O 8 HOH B 122 422 72 HOH HOH . O 8 HOH B 123 423 237 HOH HOH . O 8 HOH B 124 424 166 HOH HOH . O 8 HOH B 125 425 127 HOH HOH . O 8 HOH B 126 426 224 HOH HOH . O 8 HOH B 127 427 131 HOH HOH . O 8 HOH B 128 428 200 HOH HOH . O 8 HOH B 129 429 78 HOH HOH . O 8 HOH B 130 430 132 HOH HOH . O 8 HOH B 131 431 251 HOH HOH . O 8 HOH B 132 432 236 HOH HOH . O 8 HOH B 133 433 254 HOH HOH . O 8 HOH B 134 434 255 HOH HOH . O 8 HOH B 135 435 176 HOH HOH . O 8 HOH B 136 436 197 HOH HOH . O 8 HOH B 137 437 235 HOH HOH . O 8 HOH B 138 438 177 HOH HOH . O 8 HOH B 139 439 233 HOH HOH . O 8 HOH B 140 440 203 HOH HOH . O 8 HOH B 141 441 71 HOH HOH . O 8 HOH B 142 442 143 HOH HOH . O 8 HOH B 143 443 51 HOH HOH . O 8 HOH B 144 444 205 HOH HOH . O 8 HOH B 145 445 250 HOH HOH . O 8 HOH B 146 446 163 HOH HOH . O 8 HOH B 147 447 101 HOH HOH . O 8 HOH B 148 448 157 HOH HOH . O 8 HOH B 149 449 144 HOH HOH . O 8 HOH B 150 450 167 HOH HOH . O 8 HOH B 151 451 232 HOH HOH . O 8 HOH B 152 452 212 HOH HOH . O 8 HOH B 153 453 160 HOH HOH . O 8 HOH B 154 454 139 HOH HOH . O 8 HOH B 155 455 118 HOH HOH . O 8 HOH B 156 456 158 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id H _atom_site.label_entity_id 6 _atom_site.Cartn_x 7.877 _atom_site.Cartn_y -28.506 _atom_site.Cartn_z -22.478 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 60.22 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 206 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #