data_5DFL # _model_server_result.job_id H64_U_5Z9VMabK4xbk84Lw _model_server_result.datetime_utc '2025-07-03 23:17:42' _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 5dfl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5DFL # _exptl.entry_id 5DFL _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.43 _cell.angle_gamma 90 _cell.entry_id 5DFL _cell.length_a 146.324 _cell.length_b 37.557 _cell.length_c 61.001 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DFL _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id C _struct_conn.ptnr1_label_comp_id GLY _struct_conn.ptnr1_label_seq_id 76 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id GLY _struct_conn.ptnr1_auth_seq_id 76 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id NZ _struct_conn.ptnr2_label_comp_id LYS _struct_conn.ptnr2_label_seq_id 92 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id LYS _struct_conn.ptnr2_auth_seq_id 92 _struct_conn.ptnr2_symmetry 1_555 _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 1.271 _struct_conn.pdbx_value_order ? # _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 5DFL _atom_sites.fract_transf_matrix[1][1] 0.006834 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000051 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026626 _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] 0.016394 _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 C 3 GOL A 1 301 1 GOL GOL . D 3 GOL A 1 302 2 GOL GOL . E 3 GOL A 1 303 3 GOL GOL . F 4 HOH B 1 101 33 HOH HOH . F 4 HOH B 2 102 22 HOH HOH . F 4 HOH B 3 103 53 HOH HOH . F 4 HOH B 4 104 41 HOH HOH . F 4 HOH B 5 105 21 HOH HOH . F 4 HOH B 6 106 77 HOH HOH . F 4 HOH B 7 107 13 HOH HOH . F 4 HOH B 8 108 63 HOH HOH . F 4 HOH B 9 109 32 HOH HOH . G 4 HOH A 1 401 45 HOH HOH . G 4 HOH A 2 402 23 HOH HOH . G 4 HOH A 3 403 46 HOH HOH . G 4 HOH A 4 404 2 HOH HOH . G 4 HOH A 5 405 12 HOH HOH . G 4 HOH A 6 406 26 HOH HOH . G 4 HOH A 7 407 84 HOH HOH . G 4 HOH A 8 408 15 HOH HOH . G 4 HOH A 9 409 10 HOH HOH . G 4 HOH A 10 410 18 HOH HOH . G 4 HOH A 11 411 48 HOH HOH . G 4 HOH A 12 412 3 HOH HOH . G 4 HOH A 13 413 68 HOH HOH . G 4 HOH A 14 414 49 HOH HOH . G 4 HOH A 15 415 20 HOH HOH . G 4 HOH A 16 416 43 HOH HOH . G 4 HOH A 17 417 25 HOH HOH . G 4 HOH A 18 418 29 HOH HOH . G 4 HOH A 19 419 8 HOH HOH . G 4 HOH A 20 420 1 HOH HOH . G 4 HOH A 21 421 31 HOH HOH . G 4 HOH A 22 422 34 HOH HOH . G 4 HOH A 23 423 69 HOH HOH . G 4 HOH A 24 424 51 HOH HOH . G 4 HOH A 25 425 54 HOH HOH . G 4 HOH A 26 426 24 HOH HOH . G 4 HOH A 27 427 17 HOH HOH . G 4 HOH A 28 428 78 HOH HOH . G 4 HOH A 29 429 36 HOH HOH . G 4 HOH A 30 430 66 HOH HOH . G 4 HOH A 31 431 4 HOH HOH . G 4 HOH A 32 432 6 HOH HOH . G 4 HOH A 33 433 39 HOH HOH . G 4 HOH A 34 434 90 HOH HOH . G 4 HOH A 35 435 42 HOH HOH . G 4 HOH A 36 436 65 HOH HOH . G 4 HOH A 37 437 79 HOH HOH . G 4 HOH A 38 438 28 HOH HOH . G 4 HOH A 39 439 70 HOH HOH . G 4 HOH A 40 440 37 HOH HOH . G 4 HOH A 41 441 44 HOH HOH . G 4 HOH A 42 442 52 HOH HOH . G 4 HOH A 43 443 75 HOH HOH . G 4 HOH A 44 444 87 HOH HOH . G 4 HOH A 45 445 81 HOH HOH . G 4 HOH A 46 446 73 HOH HOH . G 4 HOH A 47 447 71 HOH HOH . G 4 HOH A 48 448 89 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 . . . C 3 -24.318 -23.982 -4.375 1 44.61 ? C1 GOL 301 A 1 HETATM 2 O O1 GOL . . . C 3 -25.151 -22.834 -4.277 1 36.06 ? O1 GOL 301 A 1 HETATM 3 C C2 GOL . . . C 3 -22.965 -23.638 -3.773 1 41.72 ? C2 GOL 301 A 1 HETATM 4 O O2 GOL . . . C 3 -22.805 -24.432 -2.599 1 51.12 ? O2 GOL 301 A 1 HETATM 5 C C3 GOL . . . C 3 -21.85 -23.924 -4.779 1 40.83 ? C3 GOL 301 A 1 HETATM 6 O O3 GOL . . . C 3 -21.764 -22.871 -5.755 1 31.75 ? O3 GOL 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #