data_4DLY # _model_server_result.job_id Hpd3M7RPWklTyA0cZ5Qcyg _model_server_result.datetime_utc '2024-11-22 20:15:33' _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 4dly # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 4DLY # _exptl.entry_id 4DLY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 154.251 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DIHYDROXY-1,4-DITHIOBUTANE _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 90 _cell.angle_gamma 120 _cell.entry_id 4DLY _cell.length_a 88.207 _cell.length_b 88.207 _cell.length_c 134.142 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DLY _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 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 ? monomeric 1 author_defined_assembly 1 PISA hexameric 6 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 A,B,C,D,E,F,G,H,I,J 2 1,2,3,4,5,6 # 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' 2_675 -y+1,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 152.779006 0 3 'crystal symmetry operation' 3_465 -x+y-1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -132.3105 76.389503 0 4 'crystal symmetry operation' 4_464 y-1,x+1,-z-1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -132.3105 76.389503 -134.142 5 'crystal symmetry operation' 5_674 x-y+1,-y+2,-z-1 1 0 0 0 -1 0 0 0 -1 0 152.779006 -134.142 6 'crystal symmetry operation' 6_554 -x,-x+y,-z-1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -134.142 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 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 OG SER 17 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc2 A O PHE 28 A PHE 28 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc3 A OD2 ASP 30 A ASP 30 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc4 A OG1 THR 35 A THR 35 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc5 A O ARG 102 A ARG 102 1_555 F CA CA . A CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc6 A OD2 ASP 105 A ASP 105 1_555 F CA CA . A CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc7 A O GLY 138 A GLY 138 1_555 G CA CA . A CA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc8 B CA CA . A CA 201 1_555 J O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc9 B CA CA . A CA 201 1_555 J O HOH . A HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc10 C MG MG . A MG 202 1_555 I O2G GNP . A GNP 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc11 C MG MG . A MG 202 1_555 I O2B GNP . A GNP 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc12 C MG MG . A MG 202 1_555 J O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc13 C MG MG . A MG 202 1_555 J O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc14 D MG MG . A MG 203 1_555 J O HOH . A HOH 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc15 D MG MG . A MG 203 1_555 J O HOH . A HOH 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc16 G CA CA . A CA 206 1_555 J O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc17 G CA CA . A CA 206 1_555 J O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc18 G CA CA . A CA 206 1_555 J O HOH . A HOH 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc19 G CA CA . A CA 206 1_555 J O HOH . A HOH 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc20 G CA CA . A CA 206 1_555 J O HOH . A HOH 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? # _chem_comp.formula 'C4 H10 O2 S2' _chem_comp.formula_weight 154.251 _chem_comp.id DTT _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DIHYDROXY-1,4-DITHIOBUTANE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,4-DITHIOTHREITOL # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag S1 C1 DTT sing 83 n n S1 HS1 DTT sing 84 n n C1 C2 DTT sing 85 n n C1 H11 DTT sing 86 n n C1 H12 DTT sing 87 n n C2 O2 DTT sing 88 n n C2 C3 DTT sing 89 n n C2 H2 DTT sing 90 n n O2 HO2 DTT sing 91 n n C3 O3 DTT sing 92 n n C3 C4 DTT sing 93 n n C3 H3 DTT sing 94 n n O3 HO3 DTT sing 95 n n C4 S4 DTT sing 96 n n C4 H41 DTT sing 97 n n C4 H42 DTT sing 98 n n S4 HS2 DTT sing 99 n n # _atom_sites.entry_id 4DLY _atom_sites.fract_transf_matrix[1][1] 0.011337 _atom_sites.fract_transf_matrix[1][2] 0.006545 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013091 _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] 0.007455 _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 CA A 1 201 202 CA CA . C 3 MG A 1 202 203 MG MG . D 3 MG A 1 203 204 MG MG . E 4 DTT A 1 204 205 DTT DTT . F 2 CA A 1 205 206 CA CA . G 2 CA A 1 206 207 CA CA . H 4 DTT A 1 207 3043 DTT DTT . I 5 GNP A 1 208 201 GNP GNP . J 6 HOH A 1 301 301 HOH HOH . J 6 HOH A 2 302 302 HOH HOH . J 6 HOH A 3 303 304 HOH HOH . J 6 HOH A 4 304 306 HOH HOH . J 6 HOH A 5 305 307 HOH HOH . J 6 HOH A 6 306 308 HOH HOH . J 6 HOH A 7 307 309 HOH HOH . J 6 HOH A 8 308 310 HOH HOH . J 6 HOH A 9 309 311 HOH HOH . J 6 HOH A 10 310 312 HOH HOH . J 6 HOH A 11 311 313 HOH HOH . J 6 HOH A 12 312 314 HOH HOH . J 6 HOH A 13 313 315 HOH HOH . J 6 HOH A 14 314 316 HOH HOH . J 6 HOH A 15 315 317 HOH HOH . J 6 HOH A 16 316 318 HOH HOH . J 6 HOH A 17 317 320 HOH HOH . J 6 HOH A 18 318 321 HOH HOH . J 6 HOH A 19 319 322 HOH HOH . J 6 HOH A 20 320 323 HOH HOH . J 6 HOH A 21 321 324 HOH HOH . J 6 HOH A 22 322 326 HOH HOH . J 6 HOH A 23 323 327 HOH HOH . J 6 HOH A 24 324 328 HOH HOH . J 6 HOH A 25 325 329 HOH HOH . J 6 HOH A 26 326 330 HOH HOH . J 6 HOH A 27 327 331 HOH HOH . J 6 HOH A 28 328 332 HOH HOH . J 6 HOH A 29 329 333 HOH HOH . J 6 HOH A 30 330 334 HOH HOH . J 6 HOH A 31 331 336 HOH HOH . J 6 HOH A 32 332 337 HOH HOH . J 6 HOH A 33 333 338 HOH HOH . J 6 HOH A 34 334 339 HOH HOH . J 6 HOH A 35 335 341 HOH HOH . J 6 HOH A 36 336 342 HOH HOH . J 6 HOH A 37 337 343 HOH HOH . J 6 HOH A 38 338 344 HOH HOH . J 6 HOH A 39 339 345 HOH HOH . J 6 HOH A 40 340 346 HOH HOH . J 6 HOH A 41 341 347 HOH HOH . J 6 HOH A 42 342 348 HOH HOH . J 6 HOH A 43 343 349 HOH HOH . J 6 HOH A 44 344 350 HOH HOH . J 6 HOH A 45 345 351 HOH HOH . J 6 HOH A 46 346 352 HOH HOH . J 6 HOH A 47 347 353 HOH HOH . J 6 HOH A 48 348 354 HOH HOH . J 6 HOH A 49 349 355 HOH HOH . J 6 HOH A 50 350 356 HOH HOH . J 6 HOH A 51 351 357 HOH HOH . J 6 HOH A 52 352 359 HOH HOH . J 6 HOH A 53 353 360 HOH HOH . J 6 HOH A 54 354 361 HOH HOH . J 6 HOH A 55 355 362 HOH HOH . J 6 HOH A 56 356 363 HOH HOH . J 6 HOH A 57 357 364 HOH HOH . J 6 HOH A 58 358 365 HOH HOH . J 6 HOH A 59 359 366 HOH HOH . J 6 HOH A 60 360 368 HOH HOH . J 6 HOH A 61 361 369 HOH HOH . J 6 HOH A 62 362 370 HOH HOH . J 6 HOH A 63 363 371 HOH HOH . J 6 HOH A 64 364 372 HOH HOH . J 6 HOH A 65 365 373 HOH HOH . J 6 HOH A 66 366 374 HOH HOH . J 6 HOH A 67 367 375 HOH HOH . J 6 HOH A 68 368 376 HOH HOH . J 6 HOH A 69 369 377 HOH HOH . J 6 HOH A 70 370 378 HOH HOH . J 6 HOH A 71 371 379 HOH HOH . J 6 HOH A 72 372 380 HOH HOH . J 6 HOH A 73 373 383 HOH HOH . J 6 HOH A 74 374 384 HOH HOH . J 6 HOH A 75 375 385 HOH HOH . J 6 HOH A 76 376 388 HOH HOH . J 6 HOH A 77 377 390 HOH HOH . J 6 HOH A 78 378 392 HOH HOH . J 6 HOH A 79 379 394 HOH HOH . J 6 HOH A 80 380 395 HOH HOH . J 6 HOH A 81 381 397 HOH HOH . J 6 HOH A 82 382 398 HOH HOH . J 6 HOH A 83 383 399 HOH HOH . J 6 HOH A 84 384 401 HOH HOH . J 6 HOH A 85 385 403 HOH HOH . J 6 HOH A 86 386 405 HOH HOH . J 6 HOH A 87 387 406 HOH HOH . J 6 HOH A 88 388 407 HOH HOH . J 6 HOH A 89 389 409 HOH HOH . J 6 HOH A 90 390 410 HOH HOH . J 6 HOH A 91 391 412 HOH HOH . J 6 HOH A 92 392 413 HOH HOH . J 6 HOH A 93 393 414 HOH HOH . J 6 HOH A 94 394 416 HOH HOH . J 6 HOH A 95 395 418 HOH HOH . J 6 HOH A 96 396 419 HOH HOH . J 6 HOH A 97 397 420 HOH HOH . J 6 HOH A 98 398 423 HOH HOH . J 6 HOH A 99 399 427 HOH HOH . J 6 HOH A 100 400 428 HOH HOH . J 6 HOH A 101 401 430 HOH HOH . J 6 HOH A 102 402 433 HOH HOH . J 6 HOH A 103 403 434 HOH HOH . J 6 HOH A 104 404 436 HOH HOH . J 6 HOH A 105 405 441 HOH HOH . J 6 HOH A 106 406 442 HOH HOH . J 6 HOH A 107 407 443 HOH HOH . J 6 HOH A 108 408 454 HOH HOH . J 6 HOH A 109 409 460 HOH HOH . J 6 HOH A 110 410 461 HOH HOH . J 6 HOH A 111 411 462 HOH HOH . J 6 HOH A 112 412 463 HOH HOH . J 6 HOH A 113 413 468 HOH HOH . J 6 HOH A 114 414 469 HOH HOH . J 6 HOH A 115 415 470 HOH HOH . J 6 HOH A 116 416 473 HOH HOH . J 6 HOH A 117 417 474 HOH HOH . J 6 HOH A 118 418 475 HOH HOH . J 6 HOH A 119 419 476 HOH HOH . J 6 HOH A 120 420 482 HOH HOH . J 6 HOH A 121 421 495 HOH HOH . J 6 HOH A 122 422 497 HOH HOH . J 6 HOH A 123 423 500 HOH HOH . J 6 HOH A 124 424 504 HOH HOH . J 6 HOH A 125 425 507 HOH HOH . J 6 HOH A 126 426 508 HOH HOH . J 6 HOH A 127 427 510 HOH HOH . J 6 HOH A 128 428 515 HOH HOH . J 6 HOH A 129 429 519 HOH HOH . J 6 HOH A 130 430 521 HOH HOH . J 6 HOH A 131 431 524 HOH HOH . J 6 HOH A 132 432 538 HOH HOH . J 6 HOH A 133 433 539 HOH HOH . J 6 HOH A 134 434 175 HOH HOH . J 6 HOH A 135 435 542 HOH HOH . J 6 HOH A 136 436 543 HOH HOH . J 6 HOH A 137 437 544 HOH HOH . J 6 HOH A 138 438 1359 HOH HOH . J 6 HOH A 139 439 1360 HOH HOH . J 6 HOH A 140 440 1361 HOH HOH . J 6 HOH A 141 441 1362 HOH HOH . J 6 HOH A 142 442 1363 HOH HOH . J 6 HOH A 143 443 1364 HOH HOH . J 6 HOH A 144 444 1365 HOH HOH . J 6 HOH A 145 445 1366 HOH HOH . J 6 HOH A 146 446 1367 HOH HOH . J 6 HOH A 147 447 1368 HOH HOH . J 6 HOH A 148 448 1369 HOH HOH . J 6 HOH A 149 449 1370 HOH HOH . J 6 HOH A 150 450 1371 HOH HOH . J 6 HOH A 151 451 1372 HOH HOH . J 6 HOH A 152 452 1373 HOH HOH . J 6 HOH A 153 453 1374 HOH HOH . J 6 HOH A 154 454 1375 HOH HOH . J 6 HOH A 155 455 1376 HOH HOH . J 6 HOH A 156 456 1377 HOH HOH . J 6 HOH A 157 457 1378 HOH HOH . J 6 HOH A 158 458 1379 HOH HOH . J 6 HOH A 159 459 1380 HOH HOH . J 6 HOH A 160 460 1381 HOH HOH . J 6 HOH A 161 461 1382 HOH HOH . J 6 HOH A 162 462 1383 HOH HOH . J 6 HOH A 163 463 1384 HOH HOH . J 6 HOH A 164 464 1385 HOH HOH . J 6 HOH A 165 465 1386 HOH HOH . J 6 HOH A 166 466 1387 HOH HOH . J 6 HOH A 167 467 1388 HOH HOH . J 6 HOH A 168 468 1389 HOH HOH . J 6 HOH A 169 469 1390 HOH HOH . J 6 HOH A 170 470 1391 HOH HOH . J 6 HOH A 171 471 1392 HOH HOH . J 6 HOH A 172 472 1393 HOH HOH . J 6 HOH A 173 473 1394 HOH HOH . J 6 HOH A 174 474 1395 HOH HOH . J 6 HOH A 175 475 1396 HOH HOH . J 6 HOH A 176 476 1397 HOH HOH . J 6 HOH A 177 477 1398 HOH HOH . J 6 HOH A 178 478 1399 HOH HOH . J 6 HOH A 179 479 1400 HOH HOH . J 6 HOH A 180 480 1401 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 S S1 DTT . . . E 4 -15.999 52.293 -66.872 1 47.54 ? S1 DTT 204 A 1 HETATM 2 C C1 DTT . . . E 4 -15.848 52.135 -68.621 1 29.66 ? C1 DTT 204 A 1 HETATM 3 C C2 DTT . . . E 4 -14.498 52.716 -68.819 1 26.3 ? C2 DTT 204 A 1 HETATM 4 O O2 DTT . . . E 4 -14.092 53.294 -67.647 1 40.31 ? O2 DTT 204 A 1 HETATM 5 C C3 DTT . . . E 4 -13.426 51.762 -69.14 1 33.85 ? C3 DTT 204 A 1 HETATM 6 O O3 DTT . . . E 4 -12.448 52.6 -69.592 1 34.83 ? O3 DTT 204 A 1 HETATM 7 C C4 DTT . . . E 4 -12.624 51.182 -68.03 1 46.18 ? C4 DTT 204 A 1 HETATM 8 S S4 DTT . . . E 4 -10.911 51.234 -68.596 1 51.02 ? S4 DTT 204 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #