data_5WDR # _model_server_result.job_id n9t3i6Nycvm9X_Tk9olIqg _model_server_result.datetime_utc '2024-11-02 12:32:32' _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 5wdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 5WDR # _exptl.entry_id 5WDR _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 117.34 _cell.angle_gamma 90 _cell.entry_id 5WDR _cell.length_a 38.562 _cell.length_b 119.106 _cell.length_c 38.57 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WDR _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 ? monomeric 1 author_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,C,D,E,I 1 1 B,F,G,H,J 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 ? 3 D N N ? 3 G 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 OG SER 21 A SER 17 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A OD1 ASP 37 A ASP 33 1_555 D NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc3 A OG1 THR 39 A THR 35 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc4 C MG MG . A MG 201 1_555 E O1G GNP . A GNP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc5 C MG MG . A MG 201 1_555 E O1B GNP . A GNP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc6 C MG MG . A MG 201 1_555 I O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc7 C MG MG . A MG 201 1_555 I O HOH . A HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc8 D NA NA . A NA 202 1_555 I O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc9 D NA NA . A NA 202 1_555 I O HOH . A HOH 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc10 D NA NA . A NA 202 1_555 I O HOH . A HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc11 D NA NA . A NA 202 1_555 J O HOH . B HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc12 D NA NA . A NA 202 1_555 J O HOH . B HOH 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc13 I O HOH . A HOH 303 1_454 G NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc14 B OG SER 21 B SER 17 1_555 F MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc15 B OD1 ASP 37 B ASP 33 1_555 G NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc16 B OD2 ASP 37 B ASP 33 1_555 G NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.065 ? metalc ? metalc17 B OG1 THR 39 B THR 35 1_555 F MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc18 F MG MG . B MG 201 1_555 H O2G GNP . B GNP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc19 F MG MG . B MG 201 1_555 H O1B GNP . B GNP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.864 ? metalc ? metalc20 F MG MG . B MG 201 1_555 J O HOH . B HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc21 F MG MG . B MG 201 1_555 J O HOH . B HOH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc22 G NA NA . B NA 202 1_555 J O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc23 G NA NA . B NA 202 1_555 J O HOH . B HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc24 G NA NA . B NA 202 1_555 J O HOH . B HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? # _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 5WDR _atom_sites.fract_transf_matrix[1][1] 0.025932 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.013409 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008396 _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] 0.029188 _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 MG A 1 201 505 MG MG . D 3 NA A 1 202 452 NA NA . E 4 GNP A 1 203 1 GNP GNP . F 2 MG B 1 201 504 MG MG . G 3 NA B 1 202 451 NA NA . H 4 GNP B 1 203 2 GNP GNP . I 5 HOH A 1 301 111 HOH HOH . I 5 HOH A 2 302 131 HOH HOH . I 5 HOH A 3 303 120 HOH HOH . I 5 HOH A 4 304 101 HOH HOH . I 5 HOH A 5 305 78 HOH HOH . I 5 HOH A 6 306 44 HOH HOH . I 5 HOH A 7 307 55 HOH HOH . I 5 HOH A 8 308 117 HOH HOH . I 5 HOH A 9 309 118 HOH HOH . I 5 HOH A 10 310 105 HOH HOH . I 5 HOH A 11 311 74 HOH HOH . I 5 HOH A 12 312 176 HOH HOH . I 5 HOH A 13 313 109 HOH HOH . I 5 HOH A 14 314 13 HOH HOH . I 5 HOH A 15 315 92 HOH HOH . I 5 HOH A 16 316 38 HOH HOH . I 5 HOH A 17 317 107 HOH HOH . I 5 HOH A 18 318 119 HOH HOH . I 5 HOH A 19 319 2 HOH HOH . I 5 HOH A 20 320 106 HOH HOH . I 5 HOH A 21 321 54 HOH HOH . I 5 HOH A 22 322 53 HOH HOH . I 5 HOH A 23 323 49 HOH HOH . I 5 HOH A 24 324 124 HOH HOH . I 5 HOH A 25 325 88 HOH HOH . I 5 HOH A 26 326 89 HOH HOH . I 5 HOH A 27 327 90 HOH HOH . I 5 HOH A 28 328 114 HOH HOH . I 5 HOH A 29 329 157 HOH HOH . I 5 HOH A 30 330 86 HOH HOH . I 5 HOH A 31 331 3 HOH HOH . I 5 HOH A 32 332 16 HOH HOH . I 5 HOH A 33 333 39 HOH HOH . I 5 HOH A 34 334 76 HOH HOH . I 5 HOH A 35 335 1 HOH HOH . I 5 HOH A 36 336 132 HOH HOH . I 5 HOH A 37 337 194 HOH HOH . I 5 HOH A 38 338 116 HOH HOH . I 5 HOH A 39 339 115 HOH HOH . I 5 HOH A 40 340 99 HOH HOH . I 5 HOH A 41 341 166 HOH HOH . I 5 HOH A 42 342 45 HOH HOH . I 5 HOH A 43 343 97 HOH HOH . I 5 HOH A 44 344 185 HOH HOH . I 5 HOH A 45 345 91 HOH HOH . I 5 HOH A 46 346 126 HOH HOH . I 5 HOH A 47 347 103 HOH HOH . I 5 HOH A 48 348 182 HOH HOH . I 5 HOH A 49 349 48 HOH HOH . I 5 HOH A 50 350 87 HOH HOH . I 5 HOH A 51 351 21 HOH HOH . I 5 HOH A 52 352 130 HOH HOH . I 5 HOH A 53 353 6 HOH HOH . I 5 HOH A 54 354 183 HOH HOH . I 5 HOH A 55 355 108 HOH HOH . I 5 HOH A 56 356 8 HOH HOH . I 5 HOH A 57 357 104 HOH HOH . I 5 HOH A 58 358 169 HOH HOH . I 5 HOH A 59 359 134 HOH HOH . I 5 HOH A 60 360 66 HOH HOH . I 5 HOH A 61 361 125 HOH HOH . I 5 HOH A 62 362 75 HOH HOH . I 5 HOH A 63 363 127 HOH HOH . I 5 HOH A 64 364 70 HOH HOH . I 5 HOH A 65 365 123 HOH HOH . I 5 HOH A 66 366 67 HOH HOH . I 5 HOH A 67 367 136 HOH HOH . I 5 HOH A 68 368 22 HOH HOH . I 5 HOH A 69 369 57 HOH HOH . I 5 HOH A 70 370 34 HOH HOH . I 5 HOH A 71 371 50 HOH HOH . I 5 HOH A 72 372 15 HOH HOH . I 5 HOH A 73 373 122 HOH HOH . I 5 HOH A 74 374 100 HOH HOH . I 5 HOH A 75 375 184 HOH HOH . I 5 HOH A 76 376 43 HOH HOH . I 5 HOH A 77 377 27 HOH HOH . I 5 HOH A 78 378 83 HOH HOH . I 5 HOH A 79 379 170 HOH HOH . I 5 HOH A 80 380 121 HOH HOH . I 5 HOH A 81 381 174 HOH HOH . I 5 HOH A 82 382 193 HOH HOH . I 5 HOH A 83 383 173 HOH HOH . I 5 HOH A 84 384 77 HOH HOH . I 5 HOH A 85 385 172 HOH HOH . I 5 HOH A 86 386 71 HOH HOH . I 5 HOH A 87 387 133 HOH HOH . I 5 HOH A 88 388 32 HOH HOH . I 5 HOH A 89 389 180 HOH HOH . I 5 HOH A 90 390 82 HOH HOH . I 5 HOH A 91 391 128 HOH HOH . I 5 HOH A 92 392 60 HOH HOH . I 5 HOH A 93 393 19 HOH HOH . I 5 HOH A 94 394 135 HOH HOH . I 5 HOH A 95 395 113 HOH HOH . I 5 HOH A 96 396 72 HOH HOH . I 5 HOH A 97 397 112 HOH HOH . I 5 HOH A 98 398 98 HOH HOH . I 5 HOH A 99 399 181 HOH HOH . I 5 HOH A 100 400 186 HOH HOH . I 5 HOH A 101 401 80 HOH HOH . I 5 HOH A 102 402 167 HOH HOH . J 5 HOH B 1 301 158 HOH HOH . J 5 HOH B 2 302 94 HOH HOH . J 5 HOH B 3 303 155 HOH HOH . J 5 HOH B 4 304 150 HOH HOH . J 5 HOH B 5 305 156 HOH HOH . J 5 HOH B 6 306 17 HOH HOH . J 5 HOH B 7 307 85 HOH HOH . J 5 HOH B 8 308 18 HOH HOH . J 5 HOH B 9 309 28 HOH HOH . J 5 HOH B 10 310 37 HOH HOH . J 5 HOH B 11 311 129 HOH HOH . J 5 HOH B 12 312 11 HOH HOH . J 5 HOH B 13 313 187 HOH HOH . J 5 HOH B 14 314 151 HOH HOH . J 5 HOH B 15 315 148 HOH HOH . J 5 HOH B 16 316 68 HOH HOH . J 5 HOH B 17 317 12 HOH HOH . J 5 HOH B 18 318 139 HOH HOH . J 5 HOH B 19 319 41 HOH HOH . J 5 HOH B 20 320 69 HOH HOH . J 5 HOH B 21 321 23 HOH HOH . J 5 HOH B 22 322 96 HOH HOH . J 5 HOH B 23 323 138 HOH HOH . J 5 HOH B 24 324 46 HOH HOH . J 5 HOH B 25 325 35 HOH HOH . J 5 HOH B 26 326 188 HOH HOH . J 5 HOH B 27 327 5 HOH HOH . J 5 HOH B 28 328 192 HOH HOH . J 5 HOH B 29 329 4 HOH HOH . J 5 HOH B 30 330 160 HOH HOH . J 5 HOH B 31 331 64 HOH HOH . J 5 HOH B 32 332 20 HOH HOH . J 5 HOH B 33 333 30 HOH HOH . J 5 HOH B 34 334 73 HOH HOH . J 5 HOH B 35 335 141 HOH HOH . J 5 HOH B 36 336 152 HOH HOH . J 5 HOH B 37 337 63 HOH HOH . J 5 HOH B 38 338 59 HOH HOH . J 5 HOH B 39 339 149 HOH HOH . J 5 HOH B 40 340 95 HOH HOH . J 5 HOH B 41 341 42 HOH HOH . J 5 HOH B 42 342 52 HOH HOH . J 5 HOH B 43 343 161 HOH HOH . J 5 HOH B 44 344 102 HOH HOH . J 5 HOH B 45 345 163 HOH HOH . J 5 HOH B 46 346 144 HOH HOH . J 5 HOH B 47 347 7 HOH HOH . J 5 HOH B 48 348 79 HOH HOH . J 5 HOH B 49 349 179 HOH HOH . J 5 HOH B 50 350 24 HOH HOH . J 5 HOH B 51 351 25 HOH HOH . J 5 HOH B 52 352 58 HOH HOH . J 5 HOH B 53 353 40 HOH HOH . J 5 HOH B 54 354 9 HOH HOH . J 5 HOH B 55 355 168 HOH HOH . J 5 HOH B 56 356 51 HOH HOH . J 5 HOH B 57 357 189 HOH HOH . J 5 HOH B 58 358 171 HOH HOH . J 5 HOH B 59 359 137 HOH HOH . J 5 HOH B 60 360 10 HOH HOH . J 5 HOH B 61 361 153 HOH HOH . J 5 HOH B 62 362 177 HOH HOH . J 5 HOH B 63 363 178 HOH HOH . J 5 HOH B 64 364 47 HOH HOH . J 5 HOH B 65 365 143 HOH HOH . J 5 HOH B 66 366 65 HOH HOH . J 5 HOH B 67 367 31 HOH HOH . J 5 HOH B 68 368 159 HOH HOH . J 5 HOH B 69 369 26 HOH HOH . J 5 HOH B 70 370 145 HOH HOH . J 5 HOH B 71 371 110 HOH HOH . J 5 HOH B 72 372 165 HOH HOH . J 5 HOH B 73 373 154 HOH HOH . J 5 HOH B 74 374 56 HOH HOH . J 5 HOH B 75 375 33 HOH HOH . J 5 HOH B 76 376 164 HOH HOH . J 5 HOH B 77 377 162 HOH HOH . J 5 HOH B 78 378 142 HOH HOH . J 5 HOH B 79 379 62 HOH HOH . J 5 HOH B 80 380 14 HOH HOH . J 5 HOH B 81 381 191 HOH HOH . J 5 HOH B 82 382 84 HOH HOH . J 5 HOH B 83 383 190 HOH HOH . J 5 HOH B 84 384 29 HOH HOH . J 5 HOH B 85 385 36 HOH HOH . J 5 HOH B 86 386 147 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 D _atom_site.label_entity_id 3 _atom_site.Cartn_x -0.764 _atom_site.Cartn_y 4.536 _atom_site.Cartn_z -12.126 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 25.64 _atom_site.pdbx_formal_charge 0 _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 17 _model_server_stats.parse_time_ms 50 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 549 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #