data_6UPO # _model_server_result.job_id DEd0KZi6Q6nS-5biAdWM2g _model_server_result.datetime_utc '2025-07-16 12:34:51' _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 6upo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":602}' # _entry.id 6UPO # _exptl.entry_id 6UPO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 134.087 _entity.id 3 _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 90 _cell.entry_id 6UPO _cell.length_a 65.929 _cell.length_b 84.59 _cell.length_c 240.354 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UPO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 metalc ? metalc1 A SG CYS 169 A CYS 133 1_555 C FE2 SF4 . A SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc2 A SG CYS 288 A CYS 252 1_555 C FE4 SF4 . A SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 A SG CYS 382 A CYS 346 1_555 C FE1 SF4 . A SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc4 C FE3 SF4 . A SF4 601 1_555 D O1B LMR . A LMR 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc5 C FE3 SF4 . A SF4 601 1_555 D O2 LMR . A LMR 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc6 B SG CYS 169 B CYS 133 1_555 E FE1 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc7 B SG CYS 288 B CYS 252 1_555 E FE3 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc8 B SG CYS 382 B CYS 346 1_555 E FE2 SF4 . B SF4 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc9 E FE4 SF4 . B SF4 601 1_555 F O1B LMR . B LMR 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc10 E FE4 SF4 . B SF4 601 1_555 F O2 LMR . B LMR 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? # _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 194 n n C1 O1B LMR sing 195 n n C1 C2 LMR sing 196 n n C2 O2 LMR sing 197 n n C2 C3 LMR sing 198 n n C3 C4 LMR sing 199 n n C4 O4A LMR sing 200 n n C4 O4B LMR doub 201 n n C2 H2 LMR sing 202 n n O2 HO2 LMR sing 203 n n C3 H3 LMR sing 204 n n C3 H3A LMR sing 205 n n O1B H4 LMR sing 206 n n O4A H5 LMR sing 207 n n # _atom_sites.entry_id 6UPO _atom_sites.fract_transf_matrix[1][1] 0.015168 _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] 0.011822 _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] 0.004161 _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 SF4 A 1 601 1 SF4 SF4 . D 3 LMR A 1 602 1 LMR LMR . E 2 SF4 B 1 601 2 SF4 SF4 . F 3 LMR B 1 602 2 LMR LMR . G 4 HOH A 1 701 5 HOH HOH . G 4 HOH A 2 702 12 HOH HOH . G 4 HOH A 3 703 3 HOH HOH . G 4 HOH A 4 704 9 HOH HOH . G 4 HOH A 5 705 11 HOH HOH . G 4 HOH A 6 706 6 HOH HOH . G 4 HOH A 7 707 7 HOH HOH . H 4 HOH B 1 701 8 HOH HOH . H 4 HOH B 2 702 1 HOH HOH . H 4 HOH B 3 703 4 HOH HOH . H 4 HOH B 4 704 2 HOH HOH . H 4 HOH B 5 705 10 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 3 24.065 5.857 -37.278 1 49.34 ? C1 LMR 602 B 1 HETATM 2 O O1A LMR . . . F 3 23.05 5.886 -38.022 1 48.95 ? O1A LMR 602 B 1 HETATM 3 O O1B LMR . . . F 3 25.166 5.435 -37.725 1 50.91 ? O1B LMR 602 B 1 HETATM 4 C C2 LMR . . . F 3 23.959 6.329 -35.832 1 43.64 ? C2 LMR 602 B 1 HETATM 5 O O2 LMR . . . F 3 24.914 5.656 -35.066 1 43.15 ? O2 LMR 602 B 1 HETATM 6 C C3 LMR . . . F 3 24.229 7.829 -35.763 1 44.52 ? C3 LMR 602 B 1 HETATM 7 C C4 LMR . . . F 3 23.302 8.473 -34.736 1 49.76 ? C4 LMR 602 B 1 HETATM 8 O O4A LMR . . . F 3 22.493 7.761 -34.083 1 47.1 ? O4A LMR 602 B 1 HETATM 9 O O4B LMR . . . F 3 23.35 9.717 -34.543 1 52.44 ? O4B LMR 602 B 1 # _model_server_stats.io_time_ms 110 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 9 #