data_3WD8 # _model_server_result.job_id opLKlf6ieWScnX8wN2Du6g _model_server_result.datetime_utc '2025-03-02 22:19:59' _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 3wd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 3WD8 # _exptl.entry_id 3WD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 90.05 _cell.angle_gamma 90 _cell.entry_id 3WD8 _cell.length_a 51.724 _cell.length_b 135.912 _cell.length_c 107.623 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WD8 _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,E,G,H 1 1 C,D,F,I,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 ? 2 E N N ? 2 F N N # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 3WD8 _atom_sites.fract_transf_matrix[1][1] 0.019333 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000016 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007358 _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] 0.009292 _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 E 2 GOL A 1 401 2 GOL GOL . F 2 GOL C 1 401 1 GOL GOL . G 3 HOH A 1 501 4 HOH HOH . G 3 HOH A 2 502 5 HOH HOH . G 3 HOH A 3 503 9 HOH HOH . G 3 HOH A 4 504 10 HOH HOH . G 3 HOH A 5 505 14 HOH HOH . G 3 HOH A 6 506 18 HOH HOH . G 3 HOH A 7 507 21 HOH HOH . G 3 HOH A 8 508 24 HOH HOH . G 3 HOH A 9 509 34 HOH HOH . G 3 HOH A 10 510 37 HOH HOH . G 3 HOH A 11 511 43 HOH HOH . G 3 HOH A 12 512 46 HOH HOH . G 3 HOH A 13 513 47 HOH HOH . G 3 HOH A 14 514 57 HOH HOH . G 3 HOH A 15 515 58 HOH HOH . G 3 HOH A 16 516 63 HOH HOH . G 3 HOH A 17 517 66 HOH HOH . G 3 HOH A 18 518 67 HOH HOH . G 3 HOH A 19 519 76 HOH HOH . G 3 HOH A 20 520 79 HOH HOH . G 3 HOH A 21 521 89 HOH HOH . G 3 HOH A 22 522 91 HOH HOH . G 3 HOH A 23 523 96 HOH HOH . G 3 HOH A 24 524 97 HOH HOH . G 3 HOH A 25 525 98 HOH HOH . G 3 HOH A 26 526 103 HOH HOH . G 3 HOH A 27 527 107 HOH HOH . G 3 HOH A 28 528 146 HOH HOH . G 3 HOH A 29 529 160 HOH HOH . G 3 HOH A 30 530 163 HOH HOH . G 3 HOH A 31 531 172 HOH HOH . G 3 HOH A 32 532 177 HOH HOH . G 3 HOH A 33 533 180 HOH HOH . G 3 HOH A 34 534 186 HOH HOH . G 3 HOH A 35 535 202 HOH HOH . G 3 HOH A 36 536 209 HOH HOH . G 3 HOH A 37 537 217 HOH HOH . G 3 HOH A 38 538 219 HOH HOH . G 3 HOH A 39 539 222 HOH HOH . G 3 HOH A 40 540 232 HOH HOH . G 3 HOH A 41 541 234 HOH HOH . G 3 HOH A 42 542 241 HOH HOH . G 3 HOH A 43 543 269 HOH HOH . G 3 HOH A 44 544 278 HOH HOH . G 3 HOH A 45 545 308 HOH HOH . G 3 HOH A 46 546 317 HOH HOH . G 3 HOH A 47 547 329 HOH HOH . G 3 HOH A 48 548 335 HOH HOH . G 3 HOH A 49 549 340 HOH HOH . G 3 HOH A 50 550 348 HOH HOH . G 3 HOH A 51 551 358 HOH HOH . G 3 HOH A 52 552 409 HOH HOH . G 3 HOH A 53 553 417 HOH HOH . G 3 HOH A 54 554 430 HOH HOH . G 3 HOH A 55 555 436 HOH HOH . G 3 HOH A 56 556 456 HOH HOH . G 3 HOH A 57 557 474 HOH HOH . G 3 HOH A 58 558 486 HOH HOH . G 3 HOH A 59 559 487 HOH HOH . G 3 HOH A 60 560 492 HOH HOH . G 3 HOH A 61 561 504 HOH HOH . G 3 HOH A 62 562 515 HOH HOH . G 3 HOH A 63 563 516 HOH HOH . G 3 HOH A 64 564 538 HOH HOH . H 3 HOH B 1 401 2 HOH HOH . H 3 HOH B 2 402 6 HOH HOH . H 3 HOH B 3 403 11 HOH HOH . H 3 HOH B 4 404 20 HOH HOH . H 3 HOH B 5 405 22 HOH HOH . H 3 HOH B 6 406 30 HOH HOH . H 3 HOH B 7 407 49 HOH HOH . H 3 HOH B 8 408 53 HOH HOH . H 3 HOH B 9 409 59 HOH HOH . H 3 HOH B 10 410 68 HOH HOH . H 3 HOH B 11 411 81 HOH HOH . H 3 HOH B 12 412 84 HOH HOH . H 3 HOH B 13 413 85 HOH HOH . H 3 HOH B 14 414 86 HOH HOH . H 3 HOH B 15 415 93 HOH HOH . H 3 HOH B 16 416 100 HOH HOH . H 3 HOH B 17 417 105 HOH HOH . H 3 HOH B 18 418 106 HOH HOH . H 3 HOH B 19 419 113 HOH HOH . H 3 HOH B 20 420 114 HOH HOH . H 3 HOH B 21 421 118 HOH HOH . H 3 HOH B 22 422 149 HOH HOH . H 3 HOH B 23 423 157 HOH HOH . H 3 HOH B 24 424 159 HOH HOH . H 3 HOH B 25 425 161 HOH HOH . H 3 HOH B 26 426 164 HOH HOH . H 3 HOH B 27 427 166 HOH HOH . H 3 HOH B 28 428 168 HOH HOH . H 3 HOH B 29 429 206 HOH HOH . H 3 HOH B 30 430 207 HOH HOH . H 3 HOH B 31 431 208 HOH HOH . H 3 HOH B 32 432 228 HOH HOH . H 3 HOH B 33 433 230 HOH HOH . H 3 HOH B 34 434 237 HOH HOH . H 3 HOH B 35 435 238 HOH HOH . H 3 HOH B 36 436 242 HOH HOH . H 3 HOH B 37 437 270 HOH HOH . H 3 HOH B 38 438 274 HOH HOH . H 3 HOH B 39 439 309 HOH HOH . H 3 HOH B 40 440 336 HOH HOH . H 3 HOH B 41 441 338 HOH HOH . H 3 HOH B 42 442 345 HOH HOH . H 3 HOH B 43 443 416 HOH HOH . H 3 HOH B 44 444 418 HOH HOH . H 3 HOH B 45 445 434 HOH HOH . H 3 HOH B 46 446 454 HOH HOH . H 3 HOH B 47 447 464 HOH HOH . H 3 HOH B 48 448 489 HOH HOH . H 3 HOH B 49 449 491 HOH HOH . H 3 HOH B 50 450 497 HOH HOH . H 3 HOH B 51 451 503 HOH HOH . H 3 HOH B 52 452 506 HOH HOH . H 3 HOH B 53 453 536 HOH HOH . H 3 HOH B 54 454 539 HOH HOH . I 3 HOH C 1 501 1 HOH HOH . I 3 HOH C 2 502 7 HOH HOH . I 3 HOH C 3 503 12 HOH HOH . I 3 HOH C 4 504 13 HOH HOH . I 3 HOH C 5 505 17 HOH HOH . I 3 HOH C 6 506 25 HOH HOH . I 3 HOH C 7 507 26 HOH HOH . I 3 HOH C 8 508 28 HOH HOH . I 3 HOH C 9 509 33 HOH HOH . I 3 HOH C 10 510 38 HOH HOH . I 3 HOH C 11 511 44 HOH HOH . I 3 HOH C 12 512 69 HOH HOH . I 3 HOH C 13 513 75 HOH HOH . I 3 HOH C 14 514 83 HOH HOH . I 3 HOH C 15 515 101 HOH HOH . I 3 HOH C 16 516 116 HOH HOH . I 3 HOH C 17 517 122 HOH HOH . I 3 HOH C 18 518 162 HOH HOH . I 3 HOH C 19 519 201 HOH HOH . I 3 HOH C 20 520 212 HOH HOH . I 3 HOH C 21 521 221 HOH HOH . I 3 HOH C 22 522 223 HOH HOH . I 3 HOH C 23 523 227 HOH HOH . I 3 HOH C 24 524 236 HOH HOH . I 3 HOH C 25 525 268 HOH HOH . I 3 HOH C 26 526 271 HOH HOH . I 3 HOH C 27 527 343 HOH HOH . I 3 HOH C 28 528 354 HOH HOH . I 3 HOH C 29 529 365 HOH HOH . I 3 HOH C 30 530 375 HOH HOH . I 3 HOH C 31 531 397 HOH HOH . I 3 HOH C 32 532 402 HOH HOH . I 3 HOH C 33 533 473 HOH HOH . I 3 HOH C 34 534 488 HOH HOH . I 3 HOH C 35 535 490 HOH HOH . I 3 HOH C 36 536 507 HOH HOH . I 3 HOH C 37 537 540 HOH HOH . J 3 HOH D 1 401 3 HOH HOH . J 3 HOH D 2 402 8 HOH HOH . J 3 HOH D 3 403 15 HOH HOH . J 3 HOH D 4 404 19 HOH HOH . J 3 HOH D 5 405 23 HOH HOH . J 3 HOH D 6 406 27 HOH HOH . J 3 HOH D 7 407 32 HOH HOH . J 3 HOH D 8 408 35 HOH HOH . J 3 HOH D 9 409 40 HOH HOH . J 3 HOH D 10 410 42 HOH HOH . J 3 HOH D 11 411 54 HOH HOH . J 3 HOH D 12 412 56 HOH HOH . J 3 HOH D 13 413 62 HOH HOH . J 3 HOH D 14 414 71 HOH HOH . J 3 HOH D 15 415 77 HOH HOH . J 3 HOH D 16 416 80 HOH HOH . J 3 HOH D 17 417 90 HOH HOH . J 3 HOH D 18 418 94 HOH HOH . J 3 HOH D 19 419 120 HOH HOH . J 3 HOH D 20 420 134 HOH HOH . J 3 HOH D 21 421 138 HOH HOH . J 3 HOH D 22 422 143 HOH HOH . J 3 HOH D 23 423 153 HOH HOH . J 3 HOH D 24 424 185 HOH HOH . J 3 HOH D 25 425 189 HOH HOH . J 3 HOH D 26 426 204 HOH HOH . J 3 HOH D 27 427 214 HOH HOH . J 3 HOH D 28 428 226 HOH HOH . J 3 HOH D 29 429 266 HOH HOH . J 3 HOH D 30 430 275 HOH HOH . J 3 HOH D 31 431 292 HOH HOH . J 3 HOH D 32 432 296 HOH HOH . J 3 HOH D 33 433 399 HOH HOH . J 3 HOH D 34 434 400 HOH HOH . J 3 HOH D 35 435 404 HOH HOH . J 3 HOH D 36 436 410 HOH HOH . J 3 HOH D 37 437 420 HOH HOH . J 3 HOH D 38 438 457 HOH HOH . J 3 HOH D 39 439 460 HOH HOH . J 3 HOH D 40 440 478 HOH HOH . J 3 HOH D 41 441 496 HOH HOH . J 3 HOH D 42 442 532 HOH HOH . J 3 HOH D 43 443 535 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 C C1 GOL . . . F 2 -2.438 67.782 39.144 1 45.43 ? C1 GOL 401 C 1 HETATM 2 O O1 GOL . . . F 2 -1.792 66.545 39.443 1 35.19 ? O1 GOL 401 C 1 HETATM 3 C C2 GOL . . . F 2 -1.473 68.91 38.821 1 38.7 ? C2 GOL 401 C 1 HETATM 4 O O2 GOL . . . F 2 -0.568 68.499 37.782 1 42.08 ? O2 GOL 401 C 1 HETATM 5 C C3 GOL . . . F 2 -0.759 69.331 40.09 1 47.82 ? C3 GOL 401 C 1 HETATM 6 O O3 GOL . . . F 2 0.059 70.501 39.959 1 44.42 ? O3 GOL 401 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 6 #