data_6TDT # _model_server_result.job_id tRvJaihmCbv8EwcARigA7g _model_server_result.datetime_utc '2024-11-19 16:27:26' _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 6tdt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":303}' # _entry.id 6TDT # _exptl.entry_id 6TDT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _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 100.175 _cell.angle_gamma 90 _cell.entry_id 6TDT _cell.length_a 69.872 _cell.length_b 71.726 _cell.length_c 72.099 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H,I,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F 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 disulf ? disulf1 A SG CYS 28 H CYS 42 1_555 A SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 119 H CYS 122 1_555 B SG CYS 9 L CYS 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf3 A SG CYS 173 H CYS 168 1_555 A SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 201 H CYS 191 1_555 A SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 53 H ASN 60 1_555 I C1 NAG . H NAG 306 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 C C GLU 8 I GLU 562 1_555 C N TYS 9 I TYS 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 C C TYS 9 I TYS 563 1_555 C N LEU 10 I LEU 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 A O LYS 174 H LYS 169 1_555 E NA NA . H NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc2 A O THR 177 H THR 172 1_555 E NA NA . H NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc3 A O PHE 215 H PHE 204 1_555 E NA NA . H NA 302 4_556 A ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc4 A O ARG 233 H ARG 221 1_555 F NA NA . H NA 303 1_555 A ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc5 A O LYS 236 H LYS 224 1_555 F NA NA . H NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc6 E NA NA . H NA 302 1_555 J O HOH . H HOH 468 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc7 E NA NA . H NA 302 1_555 J O HOH . H HOH 489 4_546 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc8 E NA NA . H NA 302 1_555 J O HOH . H HOH 576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc9 F NA NA . H NA 303 1_555 J O HOH . H HOH 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc10 F NA NA . H NA 303 1_555 J O HOH . H HOH 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc11 F NA NA . H NA 303 1_555 J O HOH . H HOH 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? metalc ? metalc12 F NA NA . H NA 303 1_555 J O HOH . H HOH 580 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? # _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 6TDT _atom_sites.fract_transf_matrix[1][1] 0.014312 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002569 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013942 _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] 0.014091 _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 D 4 PO4 H 1 301 1 PO4 PO4 . E 5 NA H 1 302 1 NA NA . F 5 NA H 1 303 2 NA NA . G 6 DMS H 1 304 1 DMS DMS . H 7 LXW H 1 305 4 LXW XXX . I 8 NAG H 1 306 1 NAG NAG . J 9 HOH H 1 401 196 HOH HOH . J 9 HOH H 2 402 219 HOH HOH . J 9 HOH H 3 403 236 HOH HOH . J 9 HOH H 4 404 292 HOH HOH . J 9 HOH H 5 405 130 HOH HOH . J 9 HOH H 6 406 309 HOH HOH . J 9 HOH H 7 407 134 HOH HOH . J 9 HOH H 8 408 98 HOH HOH . J 9 HOH H 9 409 176 HOH HOH . J 9 HOH H 10 410 111 HOH HOH . J 9 HOH H 11 411 65 HOH HOH . J 9 HOH H 12 412 82 HOH HOH . J 9 HOH H 13 413 46 HOH HOH . J 9 HOH H 14 414 222 HOH HOH . J 9 HOH H 15 415 57 HOH HOH . J 9 HOH H 16 416 158 HOH HOH . J 9 HOH H 17 417 86 HOH HOH . J 9 HOH H 18 418 148 HOH HOH . J 9 HOH H 19 419 92 HOH HOH . J 9 HOH H 20 420 24 HOH HOH . J 9 HOH H 21 421 70 HOH HOH . J 9 HOH H 22 422 306 HOH HOH . J 9 HOH H 23 423 310 HOH HOH . J 9 HOH H 24 424 187 HOH HOH . J 9 HOH H 25 425 250 HOH HOH . J 9 HOH H 26 426 142 HOH HOH . J 9 HOH H 27 427 75 HOH HOH . J 9 HOH H 28 428 189 HOH HOH . J 9 HOH H 29 429 271 HOH HOH . J 9 HOH H 30 430 185 HOH HOH . J 9 HOH H 31 431 293 HOH HOH . J 9 HOH H 32 432 213 HOH HOH . J 9 HOH H 33 433 43 HOH HOH . J 9 HOH H 34 434 227 HOH HOH . J 9 HOH H 35 435 214 HOH HOH . J 9 HOH H 36 436 71 HOH HOH . J 9 HOH H 37 437 9 HOH HOH . J 9 HOH H 38 438 52 HOH HOH . J 9 HOH H 39 439 87 HOH HOH . J 9 HOH H 40 440 55 HOH HOH . J 9 HOH H 41 441 51 HOH HOH . J 9 HOH H 42 442 32 HOH HOH . J 9 HOH H 43 443 277 HOH HOH . J 9 HOH H 44 444 50 HOH HOH . J 9 HOH H 45 445 112 HOH HOH . J 9 HOH H 46 446 231 HOH HOH . J 9 HOH H 47 447 225 HOH HOH . J 9 HOH H 48 448 48 HOH HOH . J 9 HOH H 49 449 122 HOH HOH . J 9 HOH H 50 450 37 HOH HOH . J 9 HOH H 51 451 35 HOH HOH . J 9 HOH H 52 452 295 HOH HOH . J 9 HOH H 53 453 28 HOH HOH . J 9 HOH H 54 454 18 HOH HOH . J 9 HOH H 55 455 108 HOH HOH . J 9 HOH H 56 456 151 HOH HOH . J 9 HOH H 57 457 69 HOH HOH . J 9 HOH H 58 458 20 HOH HOH . J 9 HOH H 59 459 40 HOH HOH . J 9 HOH H 60 460 174 HOH HOH . J 9 HOH H 61 461 269 HOH HOH . J 9 HOH H 62 462 244 HOH HOH . J 9 HOH H 63 463 163 HOH HOH . J 9 HOH H 64 464 188 HOH HOH . J 9 HOH H 65 465 30 HOH HOH . J 9 HOH H 66 466 62 HOH HOH . J 9 HOH H 67 467 17 HOH HOH . J 9 HOH H 68 468 85 HOH HOH . J 9 HOH H 69 469 33 HOH HOH . J 9 HOH H 70 470 22 HOH HOH . J 9 HOH H 71 471 36 HOH HOH . J 9 HOH H 72 472 58 HOH HOH . J 9 HOH H 73 473 217 HOH HOH . J 9 HOH H 74 474 104 HOH HOH . J 9 HOH H 75 475 302 HOH HOH . J 9 HOH H 76 476 27 HOH HOH . J 9 HOH H 77 477 117 HOH HOH . J 9 HOH H 78 478 289 HOH HOH . J 9 HOH H 79 479 195 HOH HOH . J 9 HOH H 80 480 275 HOH HOH . J 9 HOH H 81 481 170 HOH HOH . J 9 HOH H 82 482 12 HOH HOH . J 9 HOH H 83 483 16 HOH HOH . J 9 HOH H 84 484 118 HOH HOH . J 9 HOH H 85 485 42 HOH HOH . J 9 HOH H 86 486 261 HOH HOH . J 9 HOH H 87 487 161 HOH HOH . J 9 HOH H 88 488 10 HOH HOH . J 9 HOH H 89 489 242 HOH HOH . J 9 HOH H 90 490 38 HOH HOH . J 9 HOH H 91 491 72 HOH HOH . J 9 HOH H 92 492 21 HOH HOH . J 9 HOH H 93 493 218 HOH HOH . J 9 HOH H 94 494 153 HOH HOH . J 9 HOH H 95 495 307 HOH HOH . J 9 HOH H 96 496 8 HOH HOH . J 9 HOH H 97 497 13 HOH HOH . J 9 HOH H 98 498 25 HOH HOH . J 9 HOH H 99 499 31 HOH HOH . J 9 HOH H 100 500 97 HOH HOH . J 9 HOH H 101 501 167 HOH HOH . J 9 HOH H 102 502 146 HOH HOH . J 9 HOH H 103 503 300 HOH HOH . J 9 HOH H 104 504 44 HOH HOH . J 9 HOH H 105 505 119 HOH HOH . J 9 HOH H 106 506 100 HOH HOH . J 9 HOH H 107 507 84 HOH HOH . J 9 HOH H 108 508 26 HOH HOH . J 9 HOH H 109 509 166 HOH HOH . J 9 HOH H 110 510 14 HOH HOH . J 9 HOH H 111 511 124 HOH HOH . J 9 HOH H 112 512 157 HOH HOH . J 9 HOH H 113 513 53 HOH HOH . J 9 HOH H 114 514 3 HOH HOH . J 9 HOH H 115 515 308 HOH HOH . J 9 HOH H 116 516 15 HOH HOH . J 9 HOH H 117 517 205 HOH HOH . J 9 HOH H 118 518 59 HOH HOH . J 9 HOH H 119 519 95 HOH HOH . J 9 HOH H 120 520 294 HOH HOH . J 9 HOH H 121 521 127 HOH HOH . J 9 HOH H 122 522 270 HOH HOH . J 9 HOH H 123 523 41 HOH HOH . J 9 HOH H 124 524 129 HOH HOH . J 9 HOH H 125 525 54 HOH HOH . J 9 HOH H 126 526 243 HOH HOH . J 9 HOH H 127 527 264 HOH HOH . J 9 HOH H 128 528 147 HOH HOH . J 9 HOH H 129 529 128 HOH HOH . J 9 HOH H 130 530 93 HOH HOH . J 9 HOH H 131 531 169 HOH HOH . J 9 HOH H 132 532 237 HOH HOH . J 9 HOH H 133 533 259 HOH HOH . J 9 HOH H 134 534 11 HOH HOH . J 9 HOH H 135 535 102 HOH HOH . J 9 HOH H 136 536 190 HOH HOH . J 9 HOH H 137 537 6 HOH HOH . J 9 HOH H 138 538 125 HOH HOH . J 9 HOH H 139 539 305 HOH HOH . J 9 HOH H 140 540 152 HOH HOH . J 9 HOH H 141 541 101 HOH HOH . J 9 HOH H 142 542 251 HOH HOH . J 9 HOH H 143 543 143 HOH HOH . J 9 HOH H 144 544 4 HOH HOH . J 9 HOH H 145 545 89 HOH HOH . J 9 HOH H 146 546 228 HOH HOH . J 9 HOH H 147 547 116 HOH HOH . J 9 HOH H 148 548 133 HOH HOH . J 9 HOH H 149 549 155 HOH HOH . J 9 HOH H 150 550 80 HOH HOH . J 9 HOH H 151 551 120 HOH HOH . J 9 HOH H 152 552 96 HOH HOH . J 9 HOH H 153 553 156 HOH HOH . J 9 HOH H 154 554 139 HOH HOH . J 9 HOH H 155 555 90 HOH HOH . J 9 HOH H 156 556 254 HOH HOH . J 9 HOH H 157 557 110 HOH HOH . J 9 HOH H 158 558 301 HOH HOH . J 9 HOH H 159 559 208 HOH HOH . J 9 HOH H 160 560 141 HOH HOH . J 9 HOH H 161 561 105 HOH HOH . J 9 HOH H 162 562 77 HOH HOH . J 9 HOH H 163 563 132 HOH HOH . J 9 HOH H 164 564 160 HOH HOH . J 9 HOH H 165 565 123 HOH HOH . J 9 HOH H 166 566 164 HOH HOH . J 9 HOH H 167 567 192 HOH HOH . J 9 HOH H 168 568 91 HOH HOH . J 9 HOH H 169 569 138 HOH HOH . J 9 HOH H 170 570 168 HOH HOH . J 9 HOH H 171 571 177 HOH HOH . J 9 HOH H 172 572 60 HOH HOH . J 9 HOH H 173 573 290 HOH HOH . J 9 HOH H 174 574 232 HOH HOH . J 9 HOH H 175 575 246 HOH HOH . J 9 HOH H 176 576 88 HOH HOH . J 9 HOH H 177 577 207 HOH HOH . J 9 HOH H 178 578 68 HOH HOH . J 9 HOH H 179 579 235 HOH HOH . J 9 HOH H 180 580 245 HOH HOH . J 9 HOH H 181 581 230 HOH HOH . J 9 HOH H 182 582 299 HOH HOH . J 9 HOH H 183 583 144 HOH HOH . J 9 HOH H 184 584 29 HOH HOH . J 9 HOH H 185 585 109 HOH HOH . J 9 HOH H 186 586 239 HOH HOH . J 9 HOH H 187 587 149 HOH HOH . J 9 HOH H 188 588 296 HOH HOH . J 9 HOH H 189 589 181 HOH HOH . J 9 HOH H 190 590 159 HOH HOH . J 9 HOH H 191 591 304 HOH HOH . J 9 HOH H 192 592 140 HOH HOH . J 9 HOH H 193 593 234 HOH HOH . J 9 HOH H 194 594 253 HOH HOH . J 9 HOH H 195 595 285 HOH HOH . J 9 HOH H 196 596 145 HOH HOH . J 9 HOH H 197 597 255 HOH HOH . J 9 HOH H 198 598 268 HOH HOH . J 9 HOH H 199 599 241 HOH HOH . J 9 HOH H 200 600 172 HOH HOH . J 9 HOH H 201 601 278 HOH HOH . J 9 HOH H 202 602 154 HOH HOH . J 9 HOH H 203 603 263 HOH HOH . J 9 HOH H 204 604 173 HOH HOH . J 9 HOH H 205 605 165 HOH HOH . J 9 HOH H 206 606 94 HOH HOH . J 9 HOH H 207 607 224 HOH HOH . J 9 HOH H 208 608 106 HOH HOH . K 9 HOH L 1 101 137 HOH HOH . K 9 HOH L 2 102 199 HOH HOH . K 9 HOH L 3 103 66 HOH HOH . K 9 HOH L 4 104 180 HOH HOH . K 9 HOH L 5 105 175 HOH HOH . K 9 HOH L 6 106 61 HOH HOH . K 9 HOH L 7 107 162 HOH HOH . K 9 HOH L 8 108 63 HOH HOH . K 9 HOH L 9 109 49 HOH HOH . K 9 HOH L 10 110 248 HOH HOH . K 9 HOH L 11 111 47 HOH HOH . K 9 HOH L 12 112 64 HOH HOH . K 9 HOH L 13 113 39 HOH HOH . K 9 HOH L 14 114 81 HOH HOH . K 9 HOH L 15 115 256 HOH HOH . K 9 HOH L 16 116 19 HOH HOH . K 9 HOH L 17 117 274 HOH HOH . K 9 HOH L 18 118 73 HOH HOH . K 9 HOH L 19 119 67 HOH HOH . K 9 HOH L 20 120 74 HOH HOH . K 9 HOH L 21 121 311 HOH HOH . K 9 HOH L 22 122 56 HOH HOH . K 9 HOH L 23 123 283 HOH HOH . K 9 HOH L 24 124 284 HOH HOH . K 9 HOH L 25 125 45 HOH HOH . K 9 HOH L 26 126 204 HOH HOH . K 9 HOH L 27 127 34 HOH HOH . K 9 HOH L 28 128 202 HOH HOH . K 9 HOH L 29 129 282 HOH HOH . K 9 HOH L 30 130 150 HOH HOH . K 9 HOH L 31 131 216 HOH HOH . K 9 HOH L 32 132 247 HOH HOH . K 9 HOH L 33 133 79 HOH HOH . K 9 HOH L 34 134 131 HOH HOH . K 9 HOH L 35 135 126 HOH HOH . K 9 HOH L 36 136 276 HOH HOH . L 9 HOH I 1 601 287 HOH HOH . L 9 HOH I 2 602 249 HOH HOH . L 9 HOH I 3 603 78 HOH HOH . L 9 HOH I 4 604 215 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 F _atom_site.label_entity_id 5 _atom_site.Cartn_x 5.712 _atom_site.Cartn_y -13.46 _atom_site.Cartn_z 30.286 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 15.95 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 303 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #