data_2YDE # _model_server_result.job_id auD56sxjOJ2KAQVKQmTTlw _model_server_result.datetime_utc '2024-11-25 08:45:14' _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 2yde # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 2YDE # _exptl.entry_id 2YDE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 148.114 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-HYDROXYPENTANEDIOIC 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 2YDE _cell.length_a 86.727 _cell.length_b 86.727 _cell.length_c 146.053 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YDE _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 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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 # 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 NE2 HIS 202 A HIS 199 1_555 B FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc2 A OD2 ASP 204 A ASP 201 1_555 B FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc3 A NE2 HIS 282 A HIS 279 1_555 B FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc4 B FE FE . A FE 501 1_555 C O2 S2G . A S2G 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc5 B FE FE . A FE 501 1_555 C O3 S2G . A S2G 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc6 B FE FE . A FE 501 1_555 F O3 GOL . A GOL 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? # _chem_comp.formula 'C5 H8 O5' _chem_comp.formula_weight 148.114 _chem_comp.id S2G _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-HYDROXYPENTANEDIOIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O2 S2G sing 290 n n C1 O1 S2G doub 291 n n C1 C2 S2G sing 292 n n C3 C4 S2G sing 293 n n C3 C2 S2G sing 294 n n C4 C5 S2G sing 295 n n C5 O5 S2G sing 296 n n C5 O4 S2G doub 297 n n O3 C2 S2G sing 298 n n C2 H2 S2G sing 299 n n C3 H3 S2G sing 300 n n C3 H3A S2G sing 301 n n C4 H4 S2G sing 302 n n C4 H4A S2G sing 303 n n O5 H5 S2G sing 304 n n O3 HO3 S2G sing 305 n n O2 HO2 S2G sing 306 n n # _atom_sites.entry_id 2YDE _atom_sites.fract_transf_matrix[1][1] 0.01153 _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] 0.01153 _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] 0.006847 _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 B 2 FE A 1 501 501 FE FE . C 3 S2G A 1 601 601 S2G S2G . D 3 S2G A 1 602 602 S2G S2G . E 4 GOL A 1 603 603 GOL GOL . F 4 GOL A 1 604 604 GOL GOL . G 5 SO4 A 1 901 901 SO4 SO4 . H 5 SO4 A 1 902 902 SO4 SO4 . I 5 SO4 A 1 903 903 SO4 SO4 . J 5 SO4 A 1 905 905 SO4 SO4 . K 6 HOH A 1 2001 2001 HOH HOH . K 6 HOH A 2 2002 2002 HOH HOH . K 6 HOH A 3 2003 2003 HOH HOH . K 6 HOH A 4 2004 2004 HOH HOH . K 6 HOH A 5 2005 2005 HOH HOH . K 6 HOH A 6 2006 2006 HOH HOH . K 6 HOH A 7 2007 2007 HOH HOH . K 6 HOH A 8 2008 2008 HOH HOH . K 6 HOH A 9 2009 2009 HOH HOH . K 6 HOH A 10 2010 2010 HOH HOH . K 6 HOH A 11 2011 2011 HOH HOH . K 6 HOH A 12 2012 2012 HOH HOH . K 6 HOH A 13 2013 2013 HOH HOH . K 6 HOH A 14 2014 2014 HOH HOH . K 6 HOH A 15 2015 2015 HOH HOH . K 6 HOH A 16 2016 2016 HOH HOH . K 6 HOH A 17 2017 2017 HOH HOH . K 6 HOH A 18 2018 2018 HOH HOH . K 6 HOH A 19 2019 2019 HOH HOH . K 6 HOH A 20 2020 2020 HOH HOH . K 6 HOH A 21 2021 2021 HOH HOH . K 6 HOH A 22 2022 2022 HOH HOH . K 6 HOH A 23 2023 2023 HOH HOH . K 6 HOH A 24 2024 2024 HOH HOH . K 6 HOH A 25 2025 2025 HOH HOH . K 6 HOH A 26 2026 2026 HOH HOH . K 6 HOH A 27 2027 2027 HOH HOH . K 6 HOH A 28 2028 2028 HOH HOH . K 6 HOH A 29 2029 2029 HOH HOH . K 6 HOH A 30 2030 2030 HOH HOH . K 6 HOH A 31 2031 2031 HOH HOH . K 6 HOH A 32 2032 2032 HOH HOH . K 6 HOH A 33 2033 2033 HOH HOH . K 6 HOH A 34 2034 2034 HOH HOH . K 6 HOH A 35 2035 2035 HOH HOH . K 6 HOH A 36 2036 2036 HOH HOH . K 6 HOH A 37 2037 2037 HOH HOH . K 6 HOH A 38 2038 2038 HOH HOH . K 6 HOH A 39 2039 2039 HOH HOH . K 6 HOH A 40 2040 2040 HOH HOH . K 6 HOH A 41 2041 2041 HOH HOH . K 6 HOH A 42 2042 2042 HOH HOH . K 6 HOH A 43 2043 2043 HOH HOH . K 6 HOH A 44 2044 2044 HOH HOH . K 6 HOH A 45 2045 2045 HOH HOH . K 6 HOH A 46 2046 2046 HOH HOH . K 6 HOH A 47 2047 2047 HOH HOH . K 6 HOH A 48 2048 2048 HOH HOH . K 6 HOH A 49 2049 2049 HOH HOH . K 6 HOH A 50 2050 2050 HOH HOH . K 6 HOH A 51 2051 2051 HOH HOH . K 6 HOH A 52 2052 2052 HOH HOH . K 6 HOH A 53 2053 2053 HOH HOH . K 6 HOH A 54 2054 2054 HOH HOH . K 6 HOH A 55 2055 2055 HOH HOH . K 6 HOH A 56 2056 2056 HOH HOH . K 6 HOH A 57 2057 2057 HOH HOH . K 6 HOH A 58 2058 2058 HOH HOH . K 6 HOH A 59 2059 2059 HOH HOH . K 6 HOH A 60 2060 2060 HOH HOH . K 6 HOH A 61 2061 2061 HOH HOH . K 6 HOH A 62 2062 2062 HOH HOH . K 6 HOH A 63 2063 2063 HOH HOH . K 6 HOH A 64 2064 2064 HOH HOH . K 6 HOH A 65 2065 2065 HOH HOH . K 6 HOH A 66 2066 2066 HOH HOH . K 6 HOH A 67 2067 2067 HOH HOH . K 6 HOH A 68 2068 2068 HOH HOH . K 6 HOH A 69 2069 2069 HOH HOH . K 6 HOH A 70 2070 2070 HOH HOH . K 6 HOH A 71 2071 2071 HOH HOH . K 6 HOH A 72 2072 2072 HOH HOH . K 6 HOH A 73 2073 2073 HOH HOH . K 6 HOH A 74 2074 2074 HOH HOH . K 6 HOH A 75 2075 2075 HOH HOH . K 6 HOH A 76 2076 2076 HOH HOH . K 6 HOH A 77 2077 2077 HOH HOH . K 6 HOH A 78 2078 2078 HOH HOH . K 6 HOH A 79 2079 2079 HOH HOH . K 6 HOH A 80 2080 2080 HOH HOH . K 6 HOH A 81 2081 2081 HOH HOH . K 6 HOH A 82 2082 2082 HOH HOH . K 6 HOH A 83 2083 2083 HOH HOH . K 6 HOH A 84 2084 2084 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 S2G . . . D 3 -29.248 14.877 0.444 1 100.38 ? C1 S2G 602 A 1 HETATM 2 C C3 S2G . . . D 3 -29.104 16.719 2.109 1 99.54 ? C3 S2G 602 A 1 HETATM 3 C C4 S2G . . . D 3 -28.251 17.4 3.179 1 99.35 ? C4 S2G 602 A 1 HETATM 4 C C5 S2G . . . D 3 -29.046 18.523 3.847 1 99.73 ? C5 S2G 602 A 1 HETATM 5 O O2 S2G . . . D 3 -30.3 15.481 0.138 1 99.69 ? O2 S2G 602 A 1 HETATM 6 O O1 S2G . . . D 3 -28.869 13.782 -0.021 1 100.04 ? O1 S2G 602 A 1 HETATM 7 O O3 S2G . . . D 3 -27.146 15.994 0.888 1 100.23 ? O3 S2G 602 A 1 HETATM 8 O O5 S2G . . . D 3 -30.052 18.189 4.507 1 99.89 ? O5 S2G 602 A 1 HETATM 9 C C2 S2G . . . D 3 -28.355 15.534 1.496 1 100.1 ? C2 S2G 602 A 1 HETATM 10 O O4 S2G . . . D 3 -28.629 19.689 3.68 1 99.12 ? O4 S2G 602 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 10 #