data_3RGL # _model_server_result.job_id UCg55SiausXRZHQJ5ss6Yw _model_server_result.datetime_utc '2024-11-15 02:11:55' _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 3rgl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 3RGL # _exptl.entry_id 3RGL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 134.087 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-hydroxybutanedioic acid' _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 3RGL _cell.length_a 112.74 _cell.length_b 112.74 _cell.length_c 157.753 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RGL _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 _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 4 _struct_asym.id F _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 A C ALA 24 A ALA 0 1_555 A N MSE 25 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C MSE 25 A MSE 1 1_555 A N THR 26 A THR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C GLN 29 A GLN 5 1_555 A N MSE 30 A MSE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C MSE 30 A MSE 6 1_555 A N ILE 31 A ILE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C ASP 50 A ASP 26 1_555 A N MSE 51 A MSE 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C MSE 51 A MSE 27 1_555 A N PRO 52 A PRO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale9 A C GLY 157 A GLY 133 1_555 A N MSE 158 A MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 A C MSE 158 A MSE 134 1_555 A N GLU 159 A GLU 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 A C ALA 189 A ALA 165 1_555 A N MSE 190 A MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale12 A C MSE 190 A MSE 166 1_555 A N TYR 191 A TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 A C CYS 264 A CYS 240 1_555 A N MSE 265 A MSE 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 A C MSE 265 A MSE 241 1_555 A N LEU 266 A LEU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 A C TYR 288 A TYR 264 1_555 A N MSE 289 A MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale19 B C GLN 29 B GLN 5 1_555 B N MSE 30 B MSE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale20 B C MSE 30 B MSE 6 1_555 B N ILE 31 B ILE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale21 B C ILE 45 B ILE 21 1_555 B N MSE 46 B MSE 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale22 B C MSE 46 B MSE 22 1_555 B N GLN 47 B GLN 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale23 B C ASP 50 B ASP 26 1_555 B N MSE 51 B MSE 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale24 B C MSE 51 B MSE 27 1_555 B N PRO 52 B PRO 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale25 B C GLY 157 B GLY 133 1_555 B N MSE 158 B MSE 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale26 B C MSE 158 B MSE 134 1_555 B N GLU 159 B GLU 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale27 B C ALA 189 B ALA 165 1_555 B N MSE 190 B MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale28 B C MSE 190 B MSE 166 1_555 B N TYR 191 B TYR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale29 B C CYS 264 B CYS 240 1_555 B N MSE 265 B MSE 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale30 B C MSE 265 B MSE 241 1_555 B N LEU 266 B LEU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale31 B C TYR 288 B TYR 264 1_555 B N MSE 289 B MSE 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale32 B C MSE 289 B MSE 265 1_555 B N LEU 290 B LEU 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? # _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 243 n n C1 O1B LMR sing 244 n n C1 C2 LMR sing 245 n n C2 O2 LMR sing 246 n n C2 C3 LMR sing 247 n n C3 C4 LMR sing 248 n n C4 O4A LMR sing 249 n n C4 O4B LMR doub 250 n n C2 H2 LMR sing 251 n n O2 HO2 LMR sing 252 n n C3 H3 LMR sing 253 n n C3 H3A LMR sing 254 n n O1B H4 LMR sing 255 n n O4A H5 LMR sing 256 n n # _atom_sites.entry_id 3RGL _atom_sites.fract_transf_matrix[1][1] 0.00887 _atom_sites.fract_transf_matrix[1][2] 0.005121 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010242 _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] 0.006339 _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 GLY A 1 301 301 GLY GLY . D 3 ATP A 1 401 401 ATP ATP . E 3 ATP B 1 401 401 ATP ATP . F 4 LMR B 1 501 501 LMR LMR . G 5 HOH A 1 302 3 HOH HOH . G 5 HOH A 2 303 4 HOH HOH . G 5 HOH A 3 304 9 HOH HOH . G 5 HOH A 4 305 10 HOH HOH . G 5 HOH A 5 306 11 HOH HOH . G 5 HOH A 6 307 12 HOH HOH . G 5 HOH A 7 308 13 HOH HOH . H 5 HOH B 1 288 1 HOH HOH . H 5 HOH B 2 289 2 HOH HOH . H 5 HOH B 3 290 5 HOH HOH . H 5 HOH B 4 291 6 HOH HOH . H 5 HOH B 5 292 7 HOH HOH . H 5 HOH B 6 293 8 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 . . . F 4 -39.896 -1.938 30.276 1 82.15 ? C1 LMR 501 B 1 HETATM 2 O O1A LMR . . . F 4 -39.744 -2.714 29.296 1 77.3 ? O1A LMR 501 B 1 HETATM 3 O O1B LMR . . . F 4 -40.953 -1.265 30.347 1 84.53 ? O1B LMR 501 B 1 HETATM 4 C C2 LMR . . . F 4 -38.855 -1.8 31.371 1 74.88 ? C2 LMR 501 B 1 HETATM 5 O O2 LMR . . . F 4 -37.939 -2.876 31.498 1 54.86 ? O2 LMR 501 B 1 HETATM 6 C C3 LMR . . . F 4 -38.171 -0.425 31.424 1 83.11 ? C3 LMR 501 B 1 HETATM 7 C C4 LMR . . . F 4 -37.416 -0.029 30.159 1 80.58 ? C4 LMR 501 B 1 HETATM 8 O O4A LMR . . . F 4 -36.409 0.723 30.234 1 72.22 ? O4A LMR 501 B 1 HETATM 9 O O4B LMR . . . F 4 -37.779 -0.429 29.023 1 77.9 ? O4B LMR 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 9 #