data_3LDB # _model_server_result.job_id sCKL0opYjfF5IXNdaDSY8g _model_server_result.datetime_utc '2025-03-06 08:58:15' _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 3ldb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":337}' # _entry.id 3LDB # _exptl.entry_id 3LDB _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 5 _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 3LDB _cell.length_a 138.381 _cell.length_b 138.381 _cell.length_c 183.622 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA _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 ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N ? 4 Y N 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 disulf ? disulf1 B SG CYS 23 B CYS 23 1_555 B SG CYS 94 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf2 B SG CYS 140 B CYS 140 1_555 B SG CYS 200 B CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 C SG CYS 22 C CYS 22 1_555 C SG CYS 95 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 C SG CYS 147 C CYS 147 1_555 C SG CYS 202 C CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A SG CYS 101 A CYS 101 1_555 X HG HG . A HG 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc2 A NE2 HIS 187 A HIS 187 1_555 V FE FE . A FE 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? metalc ? metalc3 A SG CYS 207 A CYS 207 1_555 W HG HG . A HG 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc4 A NE2 HIS 273 A HIS 273 1_555 V FE FE . A FE 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? # _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 144 n n C1 C2 GOL sing 145 n n C1 H11 GOL sing 146 n n C1 H12 GOL sing 147 n n O1 HO1 GOL sing 148 n n C2 O2 GOL sing 149 n n C2 C3 GOL sing 150 n n C2 H2 GOL sing 151 n n O2 HO2 GOL sing 152 n n C3 O3 GOL sing 153 n n C3 H31 GOL sing 154 n n C3 H32 GOL sing 155 n n O3 HO3 GOL sing 156 n n # _atom_sites.entry_id 3LDB _atom_sites.fract_transf_matrix[1][1] 0.007226 _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] 0.007226 _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] 0.005446 _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 GOL A 1 335 1 GOL GOL . E 4 GOL A 1 336 2 GOL GOL . F 4 GOL A 1 337 3 GOL GOL . G 4 GOL A 1 338 4 GOL GOL . H 5 SO4 A 1 339 1 SO4 SO4 . I 5 SO4 A 1 340 3 SO4 SO4 . J 5 SO4 A 1 341 4 SO4 SO4 . K 5 SO4 A 1 342 5 SO4 SO4 . L 5 SO4 A 1 343 6 SO4 SO4 . M 5 SO4 A 1 344 8 SO4 SO4 . N 5 SO4 A 1 345 9 SO4 SO4 . O 5 SO4 A 1 346 10 SO4 SO4 . P 5 SO4 A 1 347 11 SO4 SO4 . Q 5 SO4 A 1 348 12 SO4 SO4 . R 5 SO4 A 1 349 13 SO4 SO4 . S 5 SO4 A 1 350 14 SO4 SO4 . T 5 SO4 A 1 351 18 SO4 SO4 . U 6 AKG A 1 600 600 AKG AKG . V 7 FE A 1 601 601 FE FE . W 8 HG A 1 352 1 HG HG . X 8 HG A 1 353 2 HG HG . Y 4 GOL B 1 221 6 GOL GOL . Z 5 SO4 B 1 222 7 SO4 SO4 . AA 5 SO4 B 1 223 15 SO4 SO4 . BA 5 SO4 B 1 224 19 SO4 SO4 . CA 5 SO4 C 1 222 2 SO4 SO4 . DA 5 SO4 C 1 223 16 SO4 SO4 . EA 5 SO4 C 1 224 17 SO4 SO4 . # 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 . . . F 4 -15.05 -78.984 -52.474 1 103.8 ? C1 GOL 337 A 1 HETATM 2 O O1 GOL . . . F 4 -15.903 -78.91 -53.342 1 102.75 ? O1 GOL 337 A 1 HETATM 3 C C2 GOL . . . F 4 -14.668 -80.431 -52.322 1 105.38 ? C2 GOL 337 A 1 HETATM 4 O O2 GOL . . . F 4 -14.141 -80.86 -53.575 1 106.67 ? O2 GOL 337 A 1 HETATM 5 C C3 GOL . . . F 4 -13.605 -80.62 -51.241 1 106.65 ? C3 GOL 337 A 1 HETATM 6 O O3 GOL . . . F 4 -13.29 -82.017 -51.126 1 107.36 ? O3 GOL 337 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 6 #