data_3RF1 # _model_server_result.job_id WQQscZmgRpe3i9ypBopjgA _model_server_result.datetime_utc '2024-12-18 16:59:20' _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 3rf1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":288}' # _entry.id 3RF1 # _exptl.entry_id 3RF1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 134.087 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-hydroxybutanedioic acid' _entity.pdbx_number_of_molecules 2 _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 3RF1 _cell.length_a 112.662 _cell.length_b 112.662 _cell.length_c 158.282 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RF1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,K _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 ? 2 C N N ? 2 E 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 covale ? covale1 A C ALA 24 A ALA 0 1_555 A N MSE 25 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MSE 25 A MSE 1 1_555 A N THR 26 A THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C GLN 29 A GLN 5 1_555 A N MSE 30 A MSE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A C MSE 30 A MSE 6 1_555 A N ILE 31 A ILE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale5 A C ILE 45 A ILE 21 1_555 A N MSE 46 A MSE 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C MSE 46 A MSE 22 1_555 A N GLN 47 A GLN 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale7 A C ASP 50 A ASP 26 1_555 A N MSE 51 A MSE 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale8 A C MSE 51 A MSE 27 1_555 A N PRO 52 A PRO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 A C GLY 157 A GLY 133 1_555 A N MSE 158 A MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale10 A C MSE 158 A MSE 134 1_555 A N GLU 159 A GLU 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 A C ALA 189 A ALA 165 1_555 A N MSE 190 A MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 A C MSE 190 A MSE 166 1_555 A N TYR 191 A TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 A C CYS 264 A CYS 240 1_555 A N MSE 265 A MSE 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 A C MSE 265 A MSE 241 1_555 A N LEU 266 A LEU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale15 A C TYR 288 A TYR 264 1_555 A N MSE 289 A MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale16 A C MSE 289 A MSE 265 1_555 A N LEU 290 A LEU 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale17 B C ALA 24 B ALA 0 1_555 B N MSE 25 B MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 B C MSE 25 B MSE 1 1_555 B N THR 26 B THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale19 B C GLN 29 B GLN 5 1_555 B N MSE 30 B MSE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale20 B C MSE 30 B MSE 6 1_555 B N ILE 31 B ILE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale21 B C ILE 45 B ILE 21 1_555 B N MSE 46 B MSE 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale22 B C MSE 46 B MSE 22 1_555 B N GLN 47 B GLN 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale23 B C ASP 50 B ASP 26 1_555 B N MSE 51 B MSE 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale24 B C MSE 51 B MSE 27 1_555 B N PRO 52 B PRO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale25 B C GLY 157 B GLY 133 1_555 B N MSE 158 B MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale26 B C MSE 158 B MSE 134 1_555 B N GLU 159 B GLU 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale27 B C ALA 189 B ALA 165 1_555 B N MSE 190 B MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale28 B C MSE 190 B MSE 166 1_555 B N TYR 191 B TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale29 B C CYS 264 B CYS 240 1_555 B N MSE 265 B MSE 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale30 B C MSE 265 B MSE 241 1_555 B N LEU 266 B LEU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale31 B C TYR 288 B TYR 264 1_555 B N MSE 289 B MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale32 B C MSE 289 B MSE 265 1_555 B N LEU 290 B LEU 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _chem_comp.formula 'C4 H6 O5' _chem_comp.formula_weight 134.087 _chem_comp.id LMR _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-hydroxybutanedioic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms L-Malate # 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 O1A LMR doub 207 n n C1 O1B LMR sing 208 n n C1 C2 LMR sing 209 n n C2 O2 LMR sing 210 n n C2 C3 LMR sing 211 n n C3 C4 LMR sing 212 n n C4 O4A LMR sing 213 n n C4 O4B LMR doub 214 n n C2 H2 LMR sing 215 n n O2 HO2 LMR sing 216 n n C3 H3 LMR sing 217 n n C3 H3A LMR sing 218 n n O1B H4 LMR sing 219 n n O4A H5 LMR sing 220 n n # _atom_sites.entry_id 3RF1 _atom_sites.fract_transf_matrix[1][1] 0.008876 _atom_sites.fract_transf_matrix[1][2] 0.005125 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010249 _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] 0.006318 _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 2 LMR A 1 288 2 LMR LMR . D 3 GOL A 1 289 2 GOL GOL . E 2 LMR B 1 288 1 LMR LMR . F 3 GOL B 1 289 1 GOL GOL . G 3 GOL B 1 290 3 GOL GOL . H 3 GOL B 1 291 4 GOL GOL . I 3 GOL B 1 292 5 GOL GOL . J 4 HOH A 1 290 1 HOH HOH . J 4 HOH A 2 291 2 HOH HOH . J 4 HOH A 3 292 3 HOH HOH . J 4 HOH A 4 293 4 HOH HOH . J 4 HOH A 5 294 5 HOH HOH . J 4 HOH A 6 295 6 HOH HOH . J 4 HOH A 7 296 7 HOH HOH . J 4 HOH A 8 297 10 HOH HOH . J 4 HOH A 9 298 12 HOH HOH . J 4 HOH A 10 299 14 HOH HOH . J 4 HOH A 11 300 19 HOH HOH . J 4 HOH A 12 301 20 HOH HOH . J 4 HOH A 13 302 21 HOH HOH . J 4 HOH A 14 303 23 HOH HOH . J 4 HOH A 15 304 24 HOH HOH . J 4 HOH A 16 305 25 HOH HOH . J 4 HOH A 17 306 26 HOH HOH . J 4 HOH A 18 307 27 HOH HOH . J 4 HOH A 19 308 28 HOH HOH . J 4 HOH A 20 309 30 HOH HOH . J 4 HOH A 21 310 31 HOH HOH . J 4 HOH A 22 311 33 HOH HOH . J 4 HOH A 23 312 34 HOH HOH . J 4 HOH A 24 313 35 HOH HOH . J 4 HOH A 25 314 36 HOH HOH . J 4 HOH A 26 315 37 HOH HOH . J 4 HOH A 27 316 38 HOH HOH . J 4 HOH A 28 317 39 HOH HOH . J 4 HOH A 29 318 43 HOH HOH . K 4 HOH B 1 293 8 HOH HOH . K 4 HOH B 2 294 9 HOH HOH . K 4 HOH B 3 295 11 HOH HOH . K 4 HOH B 4 296 13 HOH HOH . K 4 HOH B 5 297 15 HOH HOH . K 4 HOH B 6 298 16 HOH HOH . K 4 HOH B 7 299 17 HOH HOH . K 4 HOH B 8 300 18 HOH HOH . K 4 HOH B 9 301 22 HOH HOH . K 4 HOH B 10 302 29 HOH HOH . K 4 HOH B 11 303 32 HOH HOH . K 4 HOH B 12 304 40 HOH HOH . K 4 HOH B 13 305 41 HOH HOH . K 4 HOH B 14 306 42 HOH HOH . K 4 HOH B 15 307 44 HOH HOH . K 4 HOH B 16 308 45 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 LMR . . . C 2 10.213 -46.77 1.333 0.8 81.81 ? C1 LMR 288 A 1 HETATM 2 O O1A LMR . . . C 2 11.447 -46.98 1.216 0.8 81.21 ? O1A LMR 288 A 1 HETATM 3 O O1B LMR . . . C 2 9.438 -47.168 0.433 0.8 77.68 ? O1B LMR 288 A 1 HETATM 4 C C2 LMR . . . C 2 9.643 -46.046 2.529 0.8 80.48 ? C2 LMR 288 A 1 HETATM 5 O O2 LMR . . . C 2 10.538 -45.05 2.985 0.8 77.07 ? O2 LMR 288 A 1 HETATM 6 C C3 LMR . . . C 2 8.326 -45.403 2.099 0.8 80.32 ? C3 LMR 288 A 1 HETATM 7 C C4 LMR . . . C 2 7.26 -45.538 3.167 0.8 80.57 ? C4 LMR 288 A 1 HETATM 8 O O4A LMR . . . C 2 6.469 -44.587 3.366 0.8 78.47 ? O4A LMR 288 A 1 HETATM 9 O O4B LMR . . . C 2 7.148 -46.585 3.856 0.8 78.79 ? O4B LMR 288 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 9 #