data_5XY9 # _model_server_result.job_id eo2PZqrsY1o-G13YmGOxfA _model_server_result.datetime_utc '2025-01-25 10:54:35' _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 5xy9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5XY9 # _exptl.entry_id 5XY9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 5XY9 _cell.length_a 72.994 _cell.length_b 84.734 _cell.length_c 111.859 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XY9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _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 C C ASN 6 C ASN 319 1_555 C N TPO 7 C TPO 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 C C TPO 7 C TPO 320 1_555 C N HIS 8 C HIS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 D C ASN 6 D ASN 319 1_555 D N TPO 7 D TPO 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale4 D C TPO 7 D TPO 320 1_555 D N HIS 8 D HIS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _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 5XY9 _atom_sites.fract_transf_matrix[1][1] 0.0137 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011802 _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] 0.00894 _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 3 GOL A 1 301 1 GOL GOL . F 4 PE4 A 1 302 2 PE4 PE4 . G 5 HOH A 1 401 12 HOH HOH . G 5 HOH A 2 402 10 HOH HOH . G 5 HOH A 3 403 46 HOH HOH . G 5 HOH A 4 404 1 HOH HOH . G 5 HOH A 5 405 7 HOH HOH . G 5 HOH A 6 406 6 HOH HOH . G 5 HOH A 7 407 34 HOH HOH . G 5 HOH A 8 408 3 HOH HOH . G 5 HOH A 9 409 100 HOH HOH . G 5 HOH A 10 410 108 HOH HOH . G 5 HOH A 11 411 2 HOH HOH . G 5 HOH A 12 412 107 HOH HOH . G 5 HOH A 13 413 95 HOH HOH . G 5 HOH A 14 414 15 HOH HOH . G 5 HOH A 15 415 13 HOH HOH . G 5 HOH A 16 416 31 HOH HOH . G 5 HOH A 17 417 42 HOH HOH . G 5 HOH A 18 418 22 HOH HOH . G 5 HOH A 19 419 33 HOH HOH . G 5 HOH A 20 420 49 HOH HOH . G 5 HOH A 21 421 41 HOH HOH . G 5 HOH A 22 422 98 HOH HOH . G 5 HOH A 23 423 9 HOH HOH . G 5 HOH A 24 424 91 HOH HOH . G 5 HOH A 25 425 97 HOH HOH . G 5 HOH A 26 426 53 HOH HOH . G 5 HOH A 27 427 104 HOH HOH . G 5 HOH A 28 428 64 HOH HOH . G 5 HOH A 29 429 96 HOH HOH . G 5 HOH A 30 430 48 HOH HOH . G 5 HOH A 31 431 27 HOH HOH . G 5 HOH A 32 432 106 HOH HOH . G 5 HOH A 33 433 93 HOH HOH . G 5 HOH A 34 434 99 HOH HOH . G 5 HOH A 35 435 24 HOH HOH . G 5 HOH A 36 436 11 HOH HOH . G 5 HOH A 37 437 25 HOH HOH . G 5 HOH A 38 438 61 HOH HOH . G 5 HOH A 39 439 101 HOH HOH . G 5 HOH A 40 440 92 HOH HOH . G 5 HOH A 41 441 30 HOH HOH . G 5 HOH A 42 442 122 HOH HOH . H 5 HOH B 1 301 118 HOH HOH . H 5 HOH B 2 302 17 HOH HOH . H 5 HOH B 3 303 67 HOH HOH . H 5 HOH B 4 304 32 HOH HOH . H 5 HOH B 5 305 109 HOH HOH . H 5 HOH B 6 306 28 HOH HOH . H 5 HOH B 7 307 66 HOH HOH . H 5 HOH B 8 308 4 HOH HOH . H 5 HOH B 9 309 78 HOH HOH . H 5 HOH B 10 310 21 HOH HOH . H 5 HOH B 11 311 117 HOH HOH . H 5 HOH B 12 312 50 HOH HOH . H 5 HOH B 13 313 20 HOH HOH . H 5 HOH B 14 314 116 HOH HOH . H 5 HOH B 15 315 51 HOH HOH . H 5 HOH B 16 316 58 HOH HOH . H 5 HOH B 17 317 102 HOH HOH . H 5 HOH B 18 318 114 HOH HOH . H 5 HOH B 19 319 69 HOH HOH . H 5 HOH B 20 320 65 HOH HOH . H 5 HOH B 21 321 77 HOH HOH . H 5 HOH B 22 322 110 HOH HOH . H 5 HOH B 23 323 38 HOH HOH . H 5 HOH B 24 324 57 HOH HOH . H 5 HOH B 25 325 55 HOH HOH . H 5 HOH B 26 326 111 HOH HOH . H 5 HOH B 27 327 35 HOH HOH . H 5 HOH B 28 328 71 HOH HOH . H 5 HOH B 29 329 81 HOH HOH . H 5 HOH B 30 330 68 HOH HOH . H 5 HOH B 31 331 113 HOH HOH . H 5 HOH B 32 332 56 HOH HOH . H 5 HOH B 33 333 82 HOH HOH . H 5 HOH B 34 334 75 HOH HOH . H 5 HOH B 35 335 72 HOH HOH . H 5 HOH B 36 336 16 HOH HOH . H 5 HOH B 37 337 115 HOH HOH . H 5 HOH B 38 338 73 HOH HOH . I 5 HOH C 1 401 8 HOH HOH . I 5 HOH C 2 402 44 HOH HOH . I 5 HOH C 3 403 43 HOH HOH . I 5 HOH C 4 404 23 HOH HOH . I 5 HOH C 5 405 83 HOH HOH . I 5 HOH C 6 406 87 HOH HOH . I 5 HOH C 7 407 121 HOH HOH . I 5 HOH C 8 408 120 HOH HOH . J 5 HOH D 1 401 90 HOH HOH . J 5 HOH D 2 402 89 HOH HOH . J 5 HOH D 3 403 29 HOH HOH . J 5 HOH D 4 404 80 HOH HOH . J 5 HOH D 5 405 119 HOH HOH . J 5 HOH D 6 406 76 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 . . . E 3 53.906 -22.263 13.034 1 44.74 ? C1 GOL 301 A 1 HETATM 2 O O1 GOL . . . E 3 53.922 -21.867 14.439 1 48 ? O1 GOL 301 A 1 HETATM 3 C C2 GOL . . . E 3 53.659 -21.02 12.188 1 44.65 ? C2 GOL 301 A 1 HETATM 4 O O2 GOL . . . E 3 54.176 -19.939 12.934 1 58.67 ? O2 GOL 301 A 1 HETATM 5 C C3 GOL . . . E 3 54.231 -21.006 10.756 1 39.06 ? C3 GOL 301 A 1 HETATM 6 O O3 GOL . . . E 3 53.659 -22.091 10.066 1 38.95 ? O3 GOL 301 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 6 #