data_4YLM # _model_server_result.job_id 4FHJ4NaFfXTkKJxNryUKnw _model_server_result.datetime_utc '2024-10-20 08:14:09' _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 4ylm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 4YLM # _exptl.entry_id 4YLM _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 3 _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 4YLM _cell.length_a 124.95 _cell.length_b 124.95 _cell.length_c 107.21 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YLM _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 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 PISA trimeric 3 author_and_software_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 1 1,2,3 A,B,C,D,E 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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 124.95 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 62.475 108.209874 0 4 'crystal symmetry operation' 10_664 -y+1,-x+1,-z-1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 62.475 108.209874 -53.605 5 'crystal symmetry operation' 11_654 -x+y+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 124.95 0 -53.605 6 'crystal symmetry operation' 12_554 x,x-y,-z-1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 -53.605 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D 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 4YLM _atom_sites.fract_transf_matrix[1][1] 0.008003 _atom_sites.fract_transf_matrix[1][2] 0.004621 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009241 _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] 0.009327 _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 GOL X 1 301 1 GOL GOL . C 2 GOL X 1 302 2 GOL GOL . D 2 GOL X 1 303 3 GOL GOL . E 3 HOH X 1 401 151 HOH HOH . E 3 HOH X 2 402 83 HOH HOH . E 3 HOH X 3 403 104 HOH HOH . E 3 HOH X 4 404 164 HOH HOH . E 3 HOH X 5 405 115 HOH HOH . E 3 HOH X 6 406 163 HOH HOH . E 3 HOH X 7 407 85 HOH HOH . E 3 HOH X 8 408 11 HOH HOH . E 3 HOH X 9 409 158 HOH HOH . E 3 HOH X 10 410 116 HOH HOH . E 3 HOH X 11 411 89 HOH HOH . E 3 HOH X 12 412 145 HOH HOH . E 3 HOH X 13 413 75 HOH HOH . E 3 HOH X 14 414 81 HOH HOH . E 3 HOH X 15 415 48 HOH HOH . E 3 HOH X 16 416 148 HOH HOH . E 3 HOH X 17 417 24 HOH HOH . E 3 HOH X 18 418 149 HOH HOH . E 3 HOH X 19 419 26 HOH HOH . E 3 HOH X 20 420 23 HOH HOH . E 3 HOH X 21 421 53 HOH HOH . E 3 HOH X 22 422 94 HOH HOH . E 3 HOH X 23 423 54 HOH HOH . E 3 HOH X 24 424 52 HOH HOH . E 3 HOH X 25 425 61 HOH HOH . E 3 HOH X 26 426 80 HOH HOH . E 3 HOH X 27 427 55 HOH HOH . E 3 HOH X 28 428 156 HOH HOH . E 3 HOH X 29 429 8 HOH HOH . E 3 HOH X 30 430 64 HOH HOH . E 3 HOH X 31 431 106 HOH HOH . E 3 HOH X 32 432 90 HOH HOH . E 3 HOH X 33 433 68 HOH HOH . E 3 HOH X 34 434 154 HOH HOH . E 3 HOH X 35 435 41 HOH HOH . E 3 HOH X 36 436 96 HOH HOH . E 3 HOH X 37 437 49 HOH HOH . E 3 HOH X 38 438 144 HOH HOH . E 3 HOH X 39 439 51 HOH HOH . E 3 HOH X 40 440 112 HOH HOH . E 3 HOH X 41 441 105 HOH HOH . E 3 HOH X 42 442 101 HOH HOH . E 3 HOH X 43 443 72 HOH HOH . E 3 HOH X 44 444 146 HOH HOH . E 3 HOH X 45 445 77 HOH HOH . E 3 HOH X 46 446 170 HOH HOH . E 3 HOH X 47 447 76 HOH HOH . E 3 HOH X 48 448 147 HOH HOH . E 3 HOH X 49 449 157 HOH HOH . E 3 HOH X 50 450 86 HOH HOH . E 3 HOH X 51 451 132 HOH HOH . E 3 HOH X 52 452 79 HOH HOH . E 3 HOH X 53 453 78 HOH HOH . E 3 HOH X 54 454 127 HOH HOH . E 3 HOH X 55 455 155 HOH HOH . E 3 HOH X 56 456 103 HOH HOH . E 3 HOH X 57 457 162 HOH HOH . E 3 HOH X 58 458 73 HOH HOH . E 3 HOH X 59 459 50 HOH HOH . E 3 HOH X 60 460 150 HOH HOH . E 3 HOH X 61 461 87 HOH HOH . E 3 HOH X 62 462 69 HOH HOH . E 3 HOH X 63 463 1 HOH HOH . E 3 HOH X 64 464 84 HOH HOH . E 3 HOH X 65 465 5 HOH HOH . E 3 HOH X 66 466 100 HOH HOH . E 3 HOH X 67 467 18 HOH HOH . E 3 HOH X 68 468 19 HOH HOH . E 3 HOH X 69 469 20 HOH HOH . E 3 HOH X 70 470 21 HOH HOH . E 3 HOH X 71 471 22 HOH HOH . E 3 HOH X 72 472 25 HOH HOH . E 3 HOH X 73 473 27 HOH HOH . E 3 HOH X 74 474 28 HOH HOH . E 3 HOH X 75 475 29 HOH HOH . E 3 HOH X 76 476 30 HOH HOH . E 3 HOH X 77 477 31 HOH HOH . E 3 HOH X 78 478 32 HOH HOH . E 3 HOH X 79 479 33 HOH HOH . E 3 HOH X 80 480 34 HOH HOH . E 3 HOH X 81 481 35 HOH HOH . E 3 HOH X 82 482 37 HOH HOH . E 3 HOH X 83 483 38 HOH HOH . E 3 HOH X 84 484 39 HOH HOH . E 3 HOH X 85 485 40 HOH HOH . E 3 HOH X 86 486 42 HOH HOH . E 3 HOH X 87 487 43 HOH HOH . E 3 HOH X 88 488 44 HOH HOH . E 3 HOH X 89 489 45 HOH HOH . E 3 HOH X 90 490 46 HOH HOH . E 3 HOH X 91 491 47 HOH HOH . E 3 HOH X 92 492 56 HOH HOH . E 3 HOH X 93 493 57 HOH HOH . E 3 HOH X 94 494 59 HOH HOH . E 3 HOH X 95 495 60 HOH HOH . E 3 HOH X 96 496 62 HOH HOH . E 3 HOH X 97 497 63 HOH HOH . E 3 HOH X 98 498 65 HOH HOH . E 3 HOH X 99 499 66 HOH HOH . E 3 HOH X 100 500 67 HOH HOH . E 3 HOH X 101 501 70 HOH HOH . E 3 HOH X 102 502 71 HOH HOH . E 3 HOH X 103 503 74 HOH HOH . E 3 HOH X 104 504 82 HOH HOH . E 3 HOH X 105 505 88 HOH HOH . E 3 HOH X 106 506 91 HOH HOH . E 3 HOH X 107 507 92 HOH HOH . E 3 HOH X 108 508 97 HOH HOH . E 3 HOH X 109 509 98 HOH HOH . E 3 HOH X 110 510 99 HOH HOH . E 3 HOH X 111 511 102 HOH HOH . E 3 HOH X 112 512 107 HOH HOH . E 3 HOH X 113 513 108 HOH HOH . E 3 HOH X 114 514 109 HOH HOH . E 3 HOH X 115 515 110 HOH HOH . E 3 HOH X 116 516 111 HOH HOH . E 3 HOH X 117 517 113 HOH HOH . E 3 HOH X 118 518 114 HOH HOH . E 3 HOH X 119 519 117 HOH HOH . E 3 HOH X 120 520 118 HOH HOH . E 3 HOH X 121 521 119 HOH HOH . E 3 HOH X 122 522 120 HOH HOH . E 3 HOH X 123 523 121 HOH HOH . E 3 HOH X 124 524 122 HOH HOH . E 3 HOH X 125 525 123 HOH HOH . E 3 HOH X 126 526 124 HOH HOH . E 3 HOH X 127 527 125 HOH HOH . E 3 HOH X 128 528 126 HOH HOH . E 3 HOH X 129 529 128 HOH HOH . E 3 HOH X 130 530 131 HOH HOH . E 3 HOH X 131 531 133 HOH HOH . E 3 HOH X 132 532 134 HOH HOH . E 3 HOH X 133 533 135 HOH HOH . E 3 HOH X 134 534 136 HOH HOH . E 3 HOH X 135 535 137 HOH HOH . E 3 HOH X 136 536 138 HOH HOH . E 3 HOH X 137 537 139 HOH HOH . E 3 HOH X 138 538 140 HOH HOH . E 3 HOH X 139 539 141 HOH HOH . E 3 HOH X 140 540 142 HOH HOH . E 3 HOH X 141 541 143 HOH HOH . E 3 HOH X 142 542 153 HOH HOH . E 3 HOH X 143 543 159 HOH HOH . E 3 HOH X 144 544 160 HOH HOH . E 3 HOH X 145 545 161 HOH HOH . E 3 HOH X 146 546 165 HOH HOH . E 3 HOH X 147 547 166 HOH HOH . E 3 HOH X 148 548 167 HOH HOH . E 3 HOH X 149 549 168 HOH HOH . E 3 HOH X 150 550 169 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 . . . D 2 51.641 16.272 11.284 1 53.91 ? C1 GOL 303 X 1 HETATM 2 O O1 GOL . . . D 2 50.308 16.493 10.876 1 59.33 ? O1 GOL 303 X 1 HETATM 3 C C2 GOL . . . D 2 52.342 15.372 10.275 1 47.66 ? C2 GOL 303 X 1 HETATM 4 O O2 GOL . . . D 2 53.352 16.112 9.63 1 48.79 ? O2 GOL 303 X 1 HETATM 5 C C3 GOL . . . D 2 52.952 14.168 10.988 1 46.2 ? C3 GOL 303 X 1 HETATM 6 O O3 GOL . . . D 2 51.962 13.177 11.206 1 55.06 ? O3 GOL 303 X 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #