data_1YQK # _model_server_result.job_id CwgpZdEJsIkEPMDsWMdQjA _model_server_result.datetime_utc '2024-12-24 13:47:41' _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 1yqk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":329}' # _entry.id 1YQK # _exptl.entry_id 1YQK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _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 120 _cell.entry_id 1YQK _cell.length_a 92.358 _cell.length_b 92.358 _cell.length_c 211.312 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YQK _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 5 _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 metalc ? metalc1 B OP1 DC 6 C DC 26 1_555 D CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc2 B OP2 DC 6 C DC 26 1_555 D CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.143 ? metalc ? metalc3 C O CYS 233 A CYS 241 1_555 D CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc4 C O LEU 235 A LEU 243 1_555 D CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? metalc ? metalc5 C O VAL 238 A VAL 246 1_555 D CA CA . A CA 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? hydrog WATSON-CRICK hydrog1 A N1 DG 2 B DG 2 1_555 B N3 DC 9 C DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 2 B DG 2 1_555 B O2 DC 9 C DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 2 B DG 2 1_555 B N4 DC 9 C DC 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DT 3 B DT 3 1_555 B N1 DA 8 C DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 DT 3 B DT 3 1_555 B N6 DA 8 C DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog6 A N6 DA 4 B DA 4 1_555 B O4 DT 7 C DT 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 5 B DG 5 1_555 B N3 DC 6 C DC 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 5 B DG 5 1_555 B O2 DC 6 C DC 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 5 B DG 5 1_555 B N4 DC 6 C DC 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DA 6 B DA 6 1_555 B N3 DT 5 C DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 DA 6 B DA 6 1_555 B O4 DT 5 C DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 7 B DC 7 1_555 B N1 DG 4 C DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 7 B DC 7 1_555 B O6 DG 4 C DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 7 B DC 7 1_555 B N2 DG 4 C DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DT 9 B DT 9 1_555 B N1 DA 2 C DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O4 DT 9 B DT 9 1_555 B N6 DA 2 C DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 DG 10 B DG 10 1_555 B N3 DC 1 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 DG 10 B DG 10 1_555 B O2 DC 1 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 DG 10 B DG 10 1_555 B N4 DC 1 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 278 n n C1 C2 GOL sing 279 n n C1 H11 GOL sing 280 n n C1 H12 GOL sing 281 n n O1 HO1 GOL sing 282 n n C2 O2 GOL sing 283 n n C2 C3 GOL sing 284 n n C2 H2 GOL sing 285 n n O2 HO2 GOL sing 286 n n C3 O3 GOL sing 287 n n C3 H31 GOL sing 288 n n C3 H32 GOL sing 289 n n O3 HO3 GOL sing 290 n n # _atom_sites.entry_id 1YQK _atom_sites.fract_transf_matrix[1][1] 0.010827 _atom_sites.fract_transf_matrix[1][2] 0.006251 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012502 _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] 0.004732 _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 D 4 CA A 1 328 1 CA CA2 . E 5 GOL A 1 329 1 GOL GOL . F 6 HOH B 1 32 32 HOH HOH . F 6 HOH B 2 46 46 HOH HOH . G 6 HOH C 1 61 61 HOH HOH . G 6 HOH C 2 62 62 HOH HOH . H 6 HOH A 1 330 1 HOH HOH . H 6 HOH A 2 331 2 HOH HOH . H 6 HOH A 3 332 4 HOH HOH . H 6 HOH A 4 333 5 HOH HOH . H 6 HOH A 5 334 6 HOH HOH . H 6 HOH A 6 335 8 HOH HOH . H 6 HOH A 7 336 9 HOH HOH . H 6 HOH A 8 337 10 HOH HOH . H 6 HOH A 9 338 11 HOH HOH . H 6 HOH A 10 339 12 HOH HOH . H 6 HOH A 11 340 13 HOH HOH . H 6 HOH A 12 341 14 HOH HOH . H 6 HOH A 13 342 17 HOH HOH . H 6 HOH A 14 343 19 HOH HOH . H 6 HOH A 15 344 20 HOH HOH . H 6 HOH A 16 345 21 HOH HOH . H 6 HOH A 17 346 22 HOH HOH . H 6 HOH A 18 347 23 HOH HOH . H 6 HOH A 19 348 24 HOH HOH . H 6 HOH A 20 349 25 HOH HOH . H 6 HOH A 21 350 26 HOH HOH . H 6 HOH A 22 351 28 HOH HOH . H 6 HOH A 23 352 30 HOH HOH . H 6 HOH A 24 353 31 HOH HOH . H 6 HOH A 25 354 33 HOH HOH . H 6 HOH A 26 355 35 HOH HOH . H 6 HOH A 27 356 37 HOH HOH . H 6 HOH A 28 357 38 HOH HOH . H 6 HOH A 29 358 39 HOH HOH . H 6 HOH A 30 359 40 HOH HOH . H 6 HOH A 31 360 41 HOH HOH . H 6 HOH A 32 361 42 HOH HOH . H 6 HOH A 33 362 43 HOH HOH . H 6 HOH A 34 363 44 HOH HOH . H 6 HOH A 35 364 45 HOH HOH . H 6 HOH A 36 365 47 HOH HOH . H 6 HOH A 37 366 48 HOH HOH . H 6 HOH A 38 367 49 HOH HOH . H 6 HOH A 39 368 51 HOH HOH . H 6 HOH A 40 369 53 HOH HOH . H 6 HOH A 41 370 54 HOH HOH . H 6 HOH A 42 371 55 HOH HOH . H 6 HOH A 43 372 56 HOH HOH . H 6 HOH A 44 373 57 HOH HOH . H 6 HOH A 45 374 58 HOH HOH . H 6 HOH A 46 375 59 HOH HOH . H 6 HOH A 47 376 60 HOH HOH . H 6 HOH A 48 377 64 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 5 24.37 13.363 36.484 1 79.37 ? C1 GOL 329 A 1 HETATM 2 O O1 GOL . . . E 5 24.208 14.057 35.037 1 70.92 ? O1 GOL 329 A 1 HETATM 3 C C2 GOL . . . E 5 25.497 12.679 36.97 1 81.44 ? C2 GOL 329 A 1 HETATM 4 O O2 GOL . . . E 5 26.647 13.322 36.684 1 85.54 ? O2 GOL 329 A 1 HETATM 5 C C3 GOL . . . E 5 25.141 11.682 37.536 1 82.44 ? C3 GOL 329 A 1 HETATM 6 O O3 GOL . . . E 5 24.206 10.581 38.123 1 85.71 ? O3 GOL 329 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #