data_3SG5 # _model_server_result.job_id FAlkEm3j0NZvbNYYGfUzAQ _model_server_result.datetime_utc '2024-12-27 02:54:42' _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 3sg5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":459}' # _entry.id 3SG5 # _exptl.entry_id 3SG5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 100.19 _cell.angle_gamma 90 _cell.entry_id 3SG5 _cell.length_a 128.567 _cell.length_b 46.005 _cell.length_c 67.365 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SG5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id J _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 covale ? covale1 A C LEU 221 A LEU 221 1_555 A N1 CRO 222 A CRO 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C3 CRO 222 A CRO 223 1_555 A N VAL 223 A VAL 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? metalc ? metalc1 A OD1 ASP 320 A ASP 322 1_555 C CA CA . A CA 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc2 A OD1 ASP 322 A ASP 324 1_555 C CA CA . A CA 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc3 A OD1 ASP 324 A ASP 326 1_555 C CA CA . A CA 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc4 A O THR 326 A THR 328 1_555 C CA CA . A CA 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc5 A OE1 GLU 331 A GLU 333 1_555 C CA CA . A CA 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc6 A OE2 GLU 331 A GLU 333 1_555 C CA CA . A CA 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc7 A OD2 ASP 356 A ASP 358 1_555 E CA CA . A CA 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc8 A OD1 ASP 358 A ASP 360 1_555 E CA CA . A CA 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc9 A OD1 ASP 360 A ASP 362 1_555 E CA CA . A CA 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc10 A O THR 362 A THR 364 1_555 E CA CA . A CA 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc11 A OE2 GLU 367 A GLU 369 1_555 E CA CA . A CA 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc12 A OE1 GLU 367 A GLU 369 1_555 E CA CA . A CA 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc13 A OD2 ASP 393 A ASP 395 1_555 D CA CA . A CA 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc14 A OD2 ASP 395 A ASP 397 1_555 D CA CA . A CA 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc15 A OD1 ASN 397 A ASN 399 1_555 D CA CA . A CA 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc16 A O TYR 399 A TYR 401 1_555 D CA CA . A CA 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc17 A OE2 GLU 404 A GLU 406 1_555 D CA CA . A CA 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc18 A OE1 GLU 404 A GLU 406 1_555 D CA CA . A CA 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc19 A OD1 ASP 429 A ASP 431 1_555 B CA CA . A CA 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc20 A OD2 ASP 431 A ASP 433 1_555 B CA CA . A CA 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc21 A OD1 ASP 433 A ASP 435 1_555 B CA CA . A CA 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc22 A O GLN 435 A GLN 437 1_555 B CA CA . A CA 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc23 A OE1 GLU 440 A GLU 442 1_555 B CA CA . A CA 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc24 A OE2 GLU 440 A GLU 442 1_555 B CA CA . A CA 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc25 B CA CA . A CA 451 1_555 K O HOH . A HOH 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc26 C CA CA . A CA 452 1_555 K O HOH . A HOH 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc27 D CA CA . A CA 453 1_555 K O HOH . A HOH 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc28 E CA CA . A CA 454 1_555 K O HOH . A HOH 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? # _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 170 n n C1 C2 GOL sing 171 n n C1 H11 GOL sing 172 n n C1 H12 GOL sing 173 n n O1 HO1 GOL sing 174 n n C2 O2 GOL sing 175 n n C2 C3 GOL sing 176 n n C2 H2 GOL sing 177 n n O2 HO2 GOL sing 178 n n C3 O3 GOL sing 179 n n C3 H31 GOL sing 180 n n C3 H32 GOL sing 181 n n O3 HO3 GOL sing 182 n n # _atom_sites.entry_id 3SG5 _atom_sites.fract_transf_matrix[1][1] 0.007778 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001398 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021737 _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] 0.015082 _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 1 451 1 CA CA . C 2 CA A 1 452 2 CA CA . D 2 CA A 1 453 3 CA CA . E 2 CA A 1 454 4 CA CA . F 3 SO4 A 1 455 1 SO4 SO4 . G 3 SO4 A 1 456 2 SO4 SO4 . H 3 SO4 A 1 457 3 SO4 SO4 . I 3 SO4 A 1 458 4 SO4 SO4 . J 4 GOL A 1 459 5 GOL GOL . K 5 HOH A 1 460 2 HOH HOH . K 5 HOH A 2 461 3 HOH HOH . K 5 HOH A 3 462 4 HOH HOH . K 5 HOH A 4 463 5 HOH HOH . K 5 HOH A 5 464 6 HOH HOH . K 5 HOH A 6 465 7 HOH HOH . K 5 HOH A 7 466 8 HOH HOH . K 5 HOH A 8 467 9 HOH HOH . K 5 HOH A 9 468 10 HOH HOH . K 5 HOH A 10 469 11 HOH HOH . K 5 HOH A 11 470 12 HOH HOH . K 5 HOH A 12 471 13 HOH HOH . K 5 HOH A 13 472 14 HOH HOH . K 5 HOH A 14 473 15 HOH HOH . K 5 HOH A 15 474 16 HOH HOH . K 5 HOH A 16 475 17 HOH HOH . K 5 HOH A 17 476 18 HOH HOH . K 5 HOH A 18 477 19 HOH HOH . K 5 HOH A 19 478 20 HOH HOH . K 5 HOH A 20 479 21 HOH HOH . K 5 HOH A 21 480 22 HOH HOH . K 5 HOH A 22 481 23 HOH HOH . K 5 HOH A 23 482 24 HOH HOH . K 5 HOH A 24 483 25 HOH HOH . K 5 HOH A 25 484 26 HOH HOH . K 5 HOH A 26 485 27 HOH HOH . K 5 HOH A 27 486 28 HOH HOH . K 5 HOH A 28 487 29 HOH HOH . K 5 HOH A 29 488 30 HOH HOH . K 5 HOH A 30 489 31 HOH HOH . K 5 HOH A 31 490 32 HOH HOH . K 5 HOH A 32 491 33 HOH HOH . K 5 HOH A 33 492 34 HOH HOH . K 5 HOH A 34 493 35 HOH HOH . K 5 HOH A 35 494 36 HOH HOH . K 5 HOH A 36 495 37 HOH HOH . K 5 HOH A 37 496 38 HOH HOH . K 5 HOH A 38 497 39 HOH HOH . K 5 HOH A 39 498 40 HOH HOH . K 5 HOH A 40 499 41 HOH HOH . K 5 HOH A 41 500 42 HOH HOH . K 5 HOH A 42 501 43 HOH HOH . K 5 HOH A 43 502 44 HOH HOH . K 5 HOH A 44 503 45 HOH HOH . K 5 HOH A 45 504 46 HOH HOH . K 5 HOH A 46 505 47 HOH HOH . K 5 HOH A 47 506 48 HOH HOH . K 5 HOH A 48 507 49 HOH HOH . K 5 HOH A 49 508 50 HOH HOH . K 5 HOH A 50 509 51 HOH HOH . K 5 HOH A 51 510 52 HOH HOH . K 5 HOH A 52 511 53 HOH HOH . K 5 HOH A 53 512 54 HOH HOH . K 5 HOH A 54 513 55 HOH HOH . K 5 HOH A 55 514 56 HOH HOH . K 5 HOH A 56 515 57 HOH HOH . K 5 HOH A 57 516 58 HOH HOH . K 5 HOH A 58 517 59 HOH HOH . K 5 HOH A 59 518 60 HOH HOH . K 5 HOH A 60 519 61 HOH HOH . K 5 HOH A 61 520 62 HOH HOH . K 5 HOH A 62 521 63 HOH HOH . K 5 HOH A 63 522 64 HOH HOH . K 5 HOH A 64 523 65 HOH HOH . K 5 HOH A 65 524 66 HOH HOH . K 5 HOH A 66 525 67 HOH HOH . K 5 HOH A 67 526 68 HOH HOH . K 5 HOH A 68 527 69 HOH HOH . K 5 HOH A 69 528 70 HOH HOH . K 5 HOH A 70 529 71 HOH HOH . K 5 HOH A 71 530 72 HOH HOH . K 5 HOH A 72 531 73 HOH HOH . K 5 HOH A 73 532 74 HOH HOH . K 5 HOH A 74 533 75 HOH HOH . K 5 HOH A 75 534 76 HOH HOH . K 5 HOH A 76 535 77 HOH HOH . K 5 HOH A 77 536 78 HOH HOH . K 5 HOH A 78 537 79 HOH HOH . K 5 HOH A 79 538 80 HOH HOH . K 5 HOH A 80 539 81 HOH HOH . K 5 HOH A 81 540 82 HOH HOH . K 5 HOH A 82 541 83 HOH HOH . K 5 HOH A 83 542 84 HOH HOH . K 5 HOH A 84 543 85 HOH HOH . K 5 HOH A 85 544 86 HOH HOH . K 5 HOH A 86 545 87 HOH HOH . K 5 HOH A 87 546 88 HOH HOH . K 5 HOH A 88 547 89 HOH HOH . K 5 HOH A 89 548 90 HOH HOH . K 5 HOH A 90 549 91 HOH HOH . K 5 HOH A 91 550 92 HOH HOH . K 5 HOH A 92 551 93 HOH HOH . K 5 HOH A 93 552 94 HOH HOH . K 5 HOH A 94 553 95 HOH HOH . K 5 HOH A 95 554 96 HOH HOH . K 5 HOH A 96 555 97 HOH HOH . K 5 HOH A 97 556 98 HOH HOH . K 5 HOH A 98 557 99 HOH HOH . K 5 HOH A 99 558 100 HOH HOH . K 5 HOH A 100 559 101 HOH HOH . K 5 HOH A 101 560 102 HOH HOH . K 5 HOH A 102 561 103 HOH HOH . K 5 HOH A 103 562 104 HOH HOH . K 5 HOH A 104 563 105 HOH HOH . K 5 HOH A 105 564 106 HOH HOH . K 5 HOH A 106 565 107 HOH HOH . K 5 HOH A 107 566 108 HOH HOH . K 5 HOH A 108 567 109 HOH HOH . K 5 HOH A 109 568 110 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 . . . J 4 37.246 23.638 -16.581 1 48.71 ? C1 GOL 459 A 1 HETATM 2 O O1 GOL . . . J 4 37.453 22.258 -16.224 1 43.64 ? O1 GOL 459 A 1 HETATM 3 C C2 GOL . . . J 4 37.033 23.819 -18.084 1 50.63 ? C2 GOL 459 A 1 HETATM 4 O O2 GOL . . . J 4 36.039 22.916 -18.594 1 50.42 ? O2 GOL 459 A 1 HETATM 5 C C3 GOL . . . J 4 36.636 25.282 -18.348 1 52.06 ? C3 GOL 459 A 1 HETATM 6 O O3 GOL . . . J 4 35.421 25.677 -17.683 1 56.8 ? O3 GOL 459 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 6 #