data_4GY9 # _model_server_result.job_id eCEflf3bCJC224-FLXkK2Q _model_server_result.datetime_utc '2024-11-08 02:57:17' _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 4gy9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 4GY9 # _exptl.entry_id 4GY9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 6 _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 4GY9 _cell.length_a 96.596 _cell.length_b 96.596 _cell.length_c 112.031 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GY9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 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 author_and_software_defined_assembly 1 PISA tetrameric 4 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,B,C,D,E,F,G,H,I,J 1 1,2 A,B,C,D,E,F,G,H,I,J 2 1,3,4,5 # 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' 12_555 x,x-y,-z+1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 37.343667 3 'crystal symmetry operation' 4_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 96.596 0 0 4 'crystal symmetry operation' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z -1 0 0 0 1 0 0 0 -1 96.596 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H 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 metalc ? metalc1 A O THR 5 A THR 0 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 A O ALA 39 A ALA 34 1_555 E NA NA . A NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc3 A O PHE 64 A PHE 59 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc4 A O GLY 66 A GLY 61 1_555 D NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc5 A O SER 70 A SER 65 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc6 A O SER 70 A SER 65 1_555 G NA NA . A NA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc7 A OG SER 70 A SER 65 1_555 G NA NA . A NA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc8 A OG1 THR 71 A THR 66 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc9 A O THR 112 A THR 107 1_555 H NA NA . A NA 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc10 A O GLU 115 A GLU 110 1_555 H NA NA . A NA 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc11 A O GLY 116 A GLY 111 1_555 H NA NA . A NA 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc12 A O GLY 129 A GLY 124 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc13 C NA NA . A NA 202 1_555 J O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc14 C NA NA . A NA 202 1_555 J O HOH . A HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc15 D NA NA . A NA 203 1_555 J O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc16 D NA NA . A NA 203 1_555 J O HOH . A HOH 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc17 D NA NA . A NA 203 1_555 J O HOH . A HOH 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc18 D NA NA . A NA 203 1_555 J O HOH . A HOH 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc19 E NA NA . A NA 204 1_555 J O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc20 E NA NA . A NA 204 1_555 J O HOH . A HOH 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc21 E NA NA . A NA 204 1_555 J O HOH . A HOH 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc22 E NA NA . A NA 204 1_555 J O HOH . A HOH 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc23 E NA NA . A NA 204 1_555 J O HOH . A HOH 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc24 F NA NA . A NA 205 1_555 J O HOH . A HOH 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc25 F NA NA . A NA 205 1_555 J O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc26 F NA NA . A NA 205 1_555 J O HOH . A HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc27 G NA NA . A NA 206 1_555 J O HOH . A HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc28 G NA NA . A NA 206 1_555 J O HOH . A HOH 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc29 H NA NA . A NA 207 1_555 J O HOH . A HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc30 H NA NA . A NA 207 1_555 J O HOH . A HOH 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? # _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 4GY9 _atom_sites.fract_transf_matrix[1][1] 0.010352 _atom_sites.fract_transf_matrix[1][2] 0.005977 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011954 _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] 0.008926 _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 ZIP A 1 201 201 ZIP ZIP . C 3 NA A 1 202 1 NA NA . D 3 NA A 1 203 2 NA NA . E 3 NA A 1 204 3 NA NA . F 3 NA A 1 205 4 NA NA . G 3 NA A 1 206 5 NA NA . H 3 NA A 1 207 6 NA NA . I 4 MLI A 1 208 1 MLI MLI . J 5 HOH A 1 301 1 HOH HOH . J 5 HOH A 2 302 2 HOH HOH . J 5 HOH A 3 303 3 HOH HOH . J 5 HOH A 4 304 4 HOH HOH . J 5 HOH A 5 305 5 HOH HOH . J 5 HOH A 6 306 6 HOH HOH . J 5 HOH A 7 307 8 HOH HOH . J 5 HOH A 8 308 9 HOH HOH . J 5 HOH A 9 309 10 HOH HOH . J 5 HOH A 10 310 11 HOH HOH . J 5 HOH A 11 311 13 HOH HOH . J 5 HOH A 12 312 14 HOH HOH . J 5 HOH A 13 313 15 HOH HOH . J 5 HOH A 14 314 16 HOH HOH . J 5 HOH A 15 315 17 HOH HOH . J 5 HOH A 16 316 18 HOH HOH . J 5 HOH A 17 317 19 HOH HOH . J 5 HOH A 18 318 20 HOH HOH . J 5 HOH A 19 319 21 HOH HOH . J 5 HOH A 20 320 22 HOH HOH . J 5 HOH A 21 321 23 HOH HOH . J 5 HOH A 22 322 24 HOH HOH . J 5 HOH A 23 323 25 HOH HOH . J 5 HOH A 24 324 26 HOH HOH . J 5 HOH A 25 325 27 HOH HOH . J 5 HOH A 26 326 28 HOH HOH . J 5 HOH A 27 327 29 HOH HOH . J 5 HOH A 28 328 30 HOH HOH . J 5 HOH A 29 329 31 HOH HOH . J 5 HOH A 30 330 32 HOH HOH . J 5 HOH A 31 331 34 HOH HOH . J 5 HOH A 32 332 35 HOH HOH . J 5 HOH A 33 333 36 HOH HOH . J 5 HOH A 34 334 37 HOH HOH . J 5 HOH A 35 335 39 HOH HOH . J 5 HOH A 36 336 40 HOH HOH . J 5 HOH A 37 337 41 HOH HOH . J 5 HOH A 38 338 42 HOH HOH . J 5 HOH A 39 339 44 HOH HOH . J 5 HOH A 40 340 45 HOH HOH . J 5 HOH A 41 341 46 HOH HOH . J 5 HOH A 42 342 48 HOH HOH . J 5 HOH A 43 343 49 HOH HOH . J 5 HOH A 44 344 50 HOH HOH . J 5 HOH A 45 345 51 HOH HOH . J 5 HOH A 46 346 52 HOH HOH . J 5 HOH A 47 347 53 HOH HOH . J 5 HOH A 48 348 54 HOH HOH . J 5 HOH A 49 349 55 HOH HOH . J 5 HOH A 50 350 56 HOH HOH . J 5 HOH A 51 351 57 HOH HOH . J 5 HOH A 52 352 58 HOH HOH . J 5 HOH A 53 353 59 HOH HOH . J 5 HOH A 54 354 60 HOH HOH . J 5 HOH A 55 355 61 HOH HOH . J 5 HOH A 56 356 64 HOH HOH . J 5 HOH A 57 357 66 HOH HOH . J 5 HOH A 58 358 67 HOH HOH . J 5 HOH A 59 359 68 HOH HOH . J 5 HOH A 60 360 69 HOH HOH . J 5 HOH A 61 361 71 HOH HOH . J 5 HOH A 62 362 72 HOH HOH . J 5 HOH A 63 363 73 HOH HOH . J 5 HOH A 64 364 74 HOH HOH . J 5 HOH A 65 365 75 HOH HOH . J 5 HOH A 66 366 76 HOH HOH . J 5 HOH A 67 367 77 HOH HOH . J 5 HOH A 68 368 78 HOH HOH . J 5 HOH A 69 369 79 HOH HOH . J 5 HOH A 70 370 80 HOH HOH . J 5 HOH A 71 371 83 HOH HOH . J 5 HOH A 72 372 84 HOH HOH . J 5 HOH A 73 373 85 HOH HOH . J 5 HOH A 74 374 86 HOH HOH . J 5 HOH A 75 375 87 HOH HOH . J 5 HOH A 76 376 88 HOH HOH . J 5 HOH A 77 377 91 HOH HOH . J 5 HOH A 78 378 92 HOH HOH . J 5 HOH A 79 379 93 HOH HOH . J 5 HOH A 80 380 95 HOH HOH . J 5 HOH A 81 381 96 HOH HOH . J 5 HOH A 82 382 97 HOH HOH . J 5 HOH A 83 383 98 HOH HOH . J 5 HOH A 84 384 99 HOH HOH . J 5 HOH A 85 385 100 HOH HOH . J 5 HOH A 86 386 101 HOH HOH . J 5 HOH A 87 387 102 HOH HOH . J 5 HOH A 88 388 103 HOH HOH . J 5 HOH A 89 389 105 HOH HOH . J 5 HOH A 90 390 106 HOH HOH . J 5 HOH A 91 391 107 HOH HOH . J 5 HOH A 92 392 108 HOH HOH . J 5 HOH A 93 393 109 HOH HOH . J 5 HOH A 94 394 110 HOH HOH . J 5 HOH A 95 395 112 HOH HOH . J 5 HOH A 96 396 113 HOH HOH . J 5 HOH A 97 397 114 HOH HOH . J 5 HOH A 98 398 115 HOH HOH . J 5 HOH A 99 399 116 HOH HOH . J 5 HOH A 100 400 117 HOH HOH . J 5 HOH A 101 401 118 HOH HOH . J 5 HOH A 102 402 119 HOH HOH . J 5 HOH A 103 403 122 HOH HOH . J 5 HOH A 104 404 123 HOH HOH . J 5 HOH A 105 405 124 HOH HOH . J 5 HOH A 106 406 126 HOH HOH . J 5 HOH A 107 407 128 HOH HOH . J 5 HOH A 108 408 129 HOH HOH . J 5 HOH A 109 409 130 HOH HOH . J 5 HOH A 110 410 132 HOH HOH . J 5 HOH A 111 411 133 HOH HOH . J 5 HOH A 112 412 135 HOH HOH . J 5 HOH A 113 413 136 HOH HOH . J 5 HOH A 114 414 137 HOH HOH . J 5 HOH A 115 415 138 HOH HOH . J 5 HOH A 116 416 139 HOH HOH . J 5 HOH A 117 417 140 HOH HOH . J 5 HOH A 118 418 141 HOH HOH . J 5 HOH A 119 419 142 HOH HOH . J 5 HOH A 120 420 143 HOH HOH . J 5 HOH A 121 421 144 HOH HOH . J 5 HOH A 122 422 146 HOH HOH . J 5 HOH A 123 423 147 HOH HOH . J 5 HOH A 124 424 149 HOH HOH . J 5 HOH A 125 425 150 HOH HOH . J 5 HOH A 126 426 151 HOH HOH . J 5 HOH A 127 427 153 HOH HOH . J 5 HOH A 128 428 154 HOH HOH . J 5 HOH A 129 429 157 HOH HOH . J 5 HOH A 130 430 158 HOH HOH . J 5 HOH A 131 431 160 HOH HOH . J 5 HOH A 132 432 161 HOH HOH . J 5 HOH A 133 433 162 HOH HOH . J 5 HOH A 134 434 163 HOH HOH . J 5 HOH A 135 435 165 HOH HOH . J 5 HOH A 136 436 166 HOH HOH . J 5 HOH A 137 437 167 HOH HOH . J 5 HOH A 138 438 168 HOH HOH . J 5 HOH A 139 439 173 HOH HOH . J 5 HOH A 140 440 184 HOH HOH . J 5 HOH A 141 441 187 HOH HOH . J 5 HOH A 142 442 188 HOH HOH . J 5 HOH A 143 443 189 HOH HOH . J 5 HOH A 144 444 191 HOH HOH . J 5 HOH A 145 445 198 HOH HOH . J 5 HOH A 146 446 200 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 C _atom_site.label_entity_id 3 _atom_site.Cartn_x 41.928 _atom_site.Cartn_y 21.926 _atom_site.Cartn_z 14.413 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 37.17 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _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 10 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #