data_3DZD # _model_server_result.job_id rvqUrn1ZKeqOkvqLFkdGhw _model_server_result.datetime_utc '2025-08-31 07:56:17' _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 3dzd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1}' # _entry.id 3DZD # _exptl.entry_id 3DZD _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 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 3DZD _cell.length_a 89.897 _cell.length_b 93.105 _cell.length_c 114.163 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DZD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 3 _struct_asym.id E _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 disulf ? disulf1 A SG CYS 327 A CYS 328 1_555 A SG CYS 361 A CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 B SG CYS 327 B CYS 328 1_555 B SG CYS 361 B CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A C TRP 53 A TRP 54 1_555 A N MSE 54 A MSE 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C MSE 54 A MSE 55 1_555 A N PRO 55 A PRO 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale3 A C LEU 338 A LEU 339 1_555 A N MSE 339 A MSE 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C MSE 339 A MSE 340 1_555 A N LYS 340 A LYS 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 B C TRP 53 B TRP 54 1_555 B N MSE 54 B MSE 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 B C MSE 54 B MSE 55 1_555 B N PRO 55 B PRO 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale7 B C LEU 338 B LEU 339 1_555 B N MSE 339 B MSE 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 B C MSE 339 B MSE 340 1_555 B N LYS 340 B LYS 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? # _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 3DZD _atom_sites.fract_transf_matrix[1][1] 0.011124 _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] 0.010741 _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] 0.008759 _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 ADP A 1 370 301 ADP ADP . D 2 ADP B 1 370 300 ADP ADP . E 3 NA B 1 1 1 NA NA . F 4 HOH A 1 371 3 HOH HOH . F 4 HOH A 2 372 6 HOH HOH . F 4 HOH A 3 373 7 HOH HOH . F 4 HOH A 4 374 8 HOH HOH . F 4 HOH A 5 375 9 HOH HOH . F 4 HOH A 6 376 12 HOH HOH . F 4 HOH A 7 377 13 HOH HOH . F 4 HOH A 8 378 14 HOH HOH . F 4 HOH A 9 379 17 HOH HOH . F 4 HOH A 10 380 18 HOH HOH . F 4 HOH A 11 381 21 HOH HOH . F 4 HOH A 12 382 23 HOH HOH . F 4 HOH A 13 383 25 HOH HOH . F 4 HOH A 14 384 26 HOH HOH . F 4 HOH A 15 385 27 HOH HOH . F 4 HOH A 16 386 28 HOH HOH . F 4 HOH A 17 387 29 HOH HOH . F 4 HOH A 18 388 30 HOH HOH . F 4 HOH A 19 389 34 HOH HOH . F 4 HOH A 20 390 39 HOH HOH . F 4 HOH A 21 391 41 HOH HOH . F 4 HOH A 22 392 43 HOH HOH . F 4 HOH A 23 393 46 HOH HOH . F 4 HOH A 24 394 47 HOH HOH . F 4 HOH A 25 395 50 HOH HOH . F 4 HOH A 26 396 51 HOH HOH . F 4 HOH A 27 397 59 HOH HOH . F 4 HOH A 28 398 61 HOH HOH . F 4 HOH A 29 399 62 HOH HOH . F 4 HOH A 30 400 67 HOH HOH . F 4 HOH A 31 401 68 HOH HOH . F 4 HOH A 32 402 69 HOH HOH . F 4 HOH A 33 403 70 HOH HOH . F 4 HOH A 34 404 71 HOH HOH . F 4 HOH A 35 405 73 HOH HOH . F 4 HOH A 36 406 74 HOH HOH . F 4 HOH A 37 407 76 HOH HOH . F 4 HOH A 38 408 86 HOH HOH . F 4 HOH A 39 409 89 HOH HOH . F 4 HOH A 40 410 91 HOH HOH . F 4 HOH A 41 411 94 HOH HOH . F 4 HOH A 42 412 95 HOH HOH . F 4 HOH A 43 413 96 HOH HOH . F 4 HOH A 44 414 97 HOH HOH . F 4 HOH A 45 415 100 HOH HOH . F 4 HOH A 46 416 101 HOH HOH . F 4 HOH A 47 417 108 HOH HOH . F 4 HOH A 48 418 109 HOH HOH . F 4 HOH A 49 419 110 HOH HOH . F 4 HOH A 50 420 115 HOH HOH . F 4 HOH A 51 421 121 HOH HOH . F 4 HOH A 52 422 122 HOH HOH . F 4 HOH A 53 423 123 HOH HOH . F 4 HOH A 54 424 129 HOH HOH . F 4 HOH A 55 425 132 HOH HOH . F 4 HOH A 56 426 135 HOH HOH . F 4 HOH A 57 427 136 HOH HOH . F 4 HOH A 58 428 139 HOH HOH . F 4 HOH A 59 429 141 HOH HOH . F 4 HOH A 60 430 146 HOH HOH . F 4 HOH A 61 431 149 HOH HOH . F 4 HOH A 62 432 150 HOH HOH . F 4 HOH A 63 433 151 HOH HOH . F 4 HOH A 64 434 152 HOH HOH . F 4 HOH A 65 435 162 HOH HOH . F 4 HOH A 66 436 163 HOH HOH . F 4 HOH A 67 437 164 HOH HOH . F 4 HOH A 68 438 169 HOH HOH . F 4 HOH A 69 439 172 HOH HOH . F 4 HOH A 70 440 174 HOH HOH . F 4 HOH A 71 441 179 HOH HOH . F 4 HOH A 72 442 180 HOH HOH . F 4 HOH A 73 443 181 HOH HOH . F 4 HOH A 74 444 182 HOH HOH . F 4 HOH A 75 445 184 HOH HOH . F 4 HOH A 76 446 188 HOH HOH . F 4 HOH A 77 447 189 HOH HOH . F 4 HOH A 78 448 190 HOH HOH . F 4 HOH A 79 449 191 HOH HOH . F 4 HOH A 80 450 192 HOH HOH . F 4 HOH A 81 451 195 HOH HOH . F 4 HOH A 82 452 196 HOH HOH . F 4 HOH A 83 453 197 HOH HOH . F 4 HOH A 84 454 198 HOH HOH . F 4 HOH A 85 455 200 HOH HOH . F 4 HOH A 86 456 201 HOH HOH . F 4 HOH A 87 457 202 HOH HOH . F 4 HOH A 88 458 205 HOH HOH . F 4 HOH A 89 459 206 HOH HOH . F 4 HOH A 90 460 207 HOH HOH . F 4 HOH A 91 461 208 HOH HOH . F 4 HOH A 92 462 210 HOH HOH . F 4 HOH A 93 463 214 HOH HOH . F 4 HOH A 94 464 217 HOH HOH . F 4 HOH A 95 465 221 HOH HOH . F 4 HOH A 96 466 222 HOH HOH . F 4 HOH A 97 467 224 HOH HOH . F 4 HOH A 98 468 225 HOH HOH . F 4 HOH A 99 469 227 HOH HOH . F 4 HOH A 100 470 228 HOH HOH . F 4 HOH A 101 471 229 HOH HOH . F 4 HOH A 102 472 230 HOH HOH . F 4 HOH A 103 473 232 HOH HOH . F 4 HOH A 104 474 233 HOH HOH . F 4 HOH A 105 475 235 HOH HOH . F 4 HOH A 106 476 236 HOH HOH . F 4 HOH A 107 477 238 HOH HOH . F 4 HOH A 108 478 240 HOH HOH . F 4 HOH A 109 479 241 HOH HOH . F 4 HOH A 110 480 245 HOH HOH . F 4 HOH A 111 481 247 HOH HOH . F 4 HOH A 112 482 250 HOH HOH . F 4 HOH A 113 483 251 HOH HOH . F 4 HOH A 114 484 255 HOH HOH . F 4 HOH A 115 485 263 HOH HOH . F 4 HOH A 116 486 265 HOH HOH . F 4 HOH A 117 487 266 HOH HOH . F 4 HOH A 118 488 185 HOH HOH . G 4 HOH B 1 371 1 HOH HOH . G 4 HOH B 2 372 2 HOH HOH . G 4 HOH B 3 373 4 HOH HOH . G 4 HOH B 4 374 5 HOH HOH . G 4 HOH B 5 375 10 HOH HOH . G 4 HOH B 6 376 11 HOH HOH . G 4 HOH B 7 377 15 HOH HOH . G 4 HOH B 8 378 16 HOH HOH . G 4 HOH B 9 379 19 HOH HOH . G 4 HOH B 10 380 20 HOH HOH . G 4 HOH B 11 381 22 HOH HOH . G 4 HOH B 12 382 24 HOH HOH . G 4 HOH B 13 383 31 HOH HOH . G 4 HOH B 14 384 32 HOH HOH . G 4 HOH B 15 385 33 HOH HOH . G 4 HOH B 16 386 35 HOH HOH . G 4 HOH B 17 387 36 HOH HOH . G 4 HOH B 18 388 37 HOH HOH . G 4 HOH B 19 389 38 HOH HOH . G 4 HOH B 20 390 40 HOH HOH . G 4 HOH B 21 391 42 HOH HOH . G 4 HOH B 22 392 44 HOH HOH . G 4 HOH B 23 393 45 HOH HOH . G 4 HOH B 24 394 48 HOH HOH . G 4 HOH B 25 395 49 HOH HOH . G 4 HOH B 26 396 52 HOH HOH . G 4 HOH B 27 397 54 HOH HOH . G 4 HOH B 28 398 55 HOH HOH . G 4 HOH B 29 399 56 HOH HOH . G 4 HOH B 30 400 57 HOH HOH . G 4 HOH B 31 401 58 HOH HOH . G 4 HOH B 32 402 60 HOH HOH . G 4 HOH B 33 403 63 HOH HOH . G 4 HOH B 34 404 64 HOH HOH . G 4 HOH B 35 405 65 HOH HOH . G 4 HOH B 36 406 66 HOH HOH . G 4 HOH B 37 407 72 HOH HOH . G 4 HOH B 38 408 75 HOH HOH . G 4 HOH B 39 409 77 HOH HOH . G 4 HOH B 40 410 78 HOH HOH . G 4 HOH B 41 411 79 HOH HOH . G 4 HOH B 42 412 80 HOH HOH . G 4 HOH B 43 413 81 HOH HOH . G 4 HOH B 44 414 82 HOH HOH . G 4 HOH B 45 415 83 HOH HOH . G 4 HOH B 46 416 84 HOH HOH . G 4 HOH B 47 417 85 HOH HOH . G 4 HOH B 48 418 87 HOH HOH . G 4 HOH B 49 419 88 HOH HOH . G 4 HOH B 50 420 90 HOH HOH . G 4 HOH B 51 421 92 HOH HOH . G 4 HOH B 52 422 93 HOH HOH . G 4 HOH B 53 423 98 HOH HOH . G 4 HOH B 54 424 99 HOH HOH . G 4 HOH B 55 425 103 HOH HOH . G 4 HOH B 56 426 104 HOH HOH . G 4 HOH B 57 427 105 HOH HOH . G 4 HOH B 58 428 106 HOH HOH . G 4 HOH B 59 429 107 HOH HOH . G 4 HOH B 60 430 112 HOH HOH . G 4 HOH B 61 431 113 HOH HOH . G 4 HOH B 62 432 114 HOH HOH . G 4 HOH B 63 433 119 HOH HOH . G 4 HOH B 64 434 120 HOH HOH . G 4 HOH B 65 435 130 HOH HOH . G 4 HOH B 66 436 131 HOH HOH . G 4 HOH B 67 437 133 HOH HOH . G 4 HOH B 68 438 134 HOH HOH . G 4 HOH B 69 439 137 HOH HOH . G 4 HOH B 70 440 138 HOH HOH . G 4 HOH B 71 441 140 HOH HOH . G 4 HOH B 72 442 142 HOH HOH . G 4 HOH B 73 443 143 HOH HOH . G 4 HOH B 74 444 144 HOH HOH . G 4 HOH B 75 445 145 HOH HOH . G 4 HOH B 76 446 147 HOH HOH . G 4 HOH B 77 447 148 HOH HOH . G 4 HOH B 78 448 153 HOH HOH . G 4 HOH B 79 449 154 HOH HOH . G 4 HOH B 80 450 155 HOH HOH . G 4 HOH B 81 451 156 HOH HOH . G 4 HOH B 82 452 157 HOH HOH . G 4 HOH B 83 453 158 HOH HOH . G 4 HOH B 84 454 159 HOH HOH . G 4 HOH B 85 455 160 HOH HOH . G 4 HOH B 86 456 161 HOH HOH . G 4 HOH B 87 457 166 HOH HOH . G 4 HOH B 88 458 167 HOH HOH . G 4 HOH B 89 459 170 HOH HOH . G 4 HOH B 90 460 173 HOH HOH . G 4 HOH B 91 461 175 HOH HOH . G 4 HOH B 92 462 176 HOH HOH . G 4 HOH B 93 463 177 HOH HOH . G 4 HOH B 94 464 178 HOH HOH . G 4 HOH B 95 465 183 HOH HOH . G 4 HOH B 96 467 186 HOH HOH . G 4 HOH B 97 468 187 HOH HOH . G 4 HOH B 98 469 193 HOH HOH . G 4 HOH B 99 470 194 HOH HOH . G 4 HOH B 100 471 199 HOH HOH . G 4 HOH B 101 472 203 HOH HOH . G 4 HOH B 102 473 204 HOH HOH . G 4 HOH B 103 474 209 HOH HOH . G 4 HOH B 104 475 211 HOH HOH . G 4 HOH B 105 476 212 HOH HOH . G 4 HOH B 106 477 213 HOH HOH . G 4 HOH B 107 478 215 HOH HOH . G 4 HOH B 108 479 216 HOH HOH . G 4 HOH B 109 480 218 HOH HOH . G 4 HOH B 110 481 219 HOH HOH . G 4 HOH B 111 482 220 HOH HOH . G 4 HOH B 112 483 223 HOH HOH . G 4 HOH B 113 484 226 HOH HOH . G 4 HOH B 114 485 231 HOH HOH . G 4 HOH B 115 486 234 HOH HOH . G 4 HOH B 116 487 237 HOH HOH . G 4 HOH B 117 488 243 HOH HOH . G 4 HOH B 118 489 246 HOH HOH . G 4 HOH B 119 490 248 HOH HOH . G 4 HOH B 120 491 249 HOH HOH . G 4 HOH B 121 492 252 HOH HOH . G 4 HOH B 122 493 253 HOH HOH . G 4 HOH B 123 494 254 HOH HOH . G 4 HOH B 124 495 256 HOH HOH . G 4 HOH B 125 496 257 HOH HOH . G 4 HOH B 126 497 258 HOH HOH . G 4 HOH B 127 498 259 HOH HOH . G 4 HOH B 128 499 260 HOH HOH . G 4 HOH B 129 500 261 HOH HOH . G 4 HOH B 130 501 262 HOH HOH . G 4 HOH B 131 502 264 HOH HOH . G 4 HOH B 132 503 267 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 E _atom_site.label_entity_id 3 _atom_site.Cartn_x -33.4 _atom_site.Cartn_y 8.66 _atom_site.Cartn_z 43.929 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 45.17 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 65 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 609 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #