data_2YMX # _model_server_result.job_id Img_Dq6ep6anmVfe3NjeQA _model_server_result.datetime_utc '2025-04-22 01:09:34' _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 2ymx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1214}' # _entry.id 2YMX # _exptl.entry_id 2YMX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 90 _cell.entry_id 2YMX _cell.length_a 69.95 _cell.length_b 129.111 _cell.length_c 99.264 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YMX _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 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 _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 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 22 H CYS 22 1_555 A SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 151 H CYS 151 1_555 A SG CYS 206 H CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 B SG CYS 23 L CYS 23 1_555 B SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? disulf ? disulf4 B SG CYS 134 L CYS 134 1_555 B SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 2YMX _atom_sites.fract_transf_matrix[1][1] 0.014296 _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] 0.007745 _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] 0.010074 _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 3 GOL L 1 1214 1214 GOL GOL . D 4 HOH H 1 2001 2001 HOH HOH . D 4 HOH H 2 2002 2002 HOH HOH . D 4 HOH H 3 2003 2003 HOH HOH . D 4 HOH H 4 2004 2004 HOH HOH . D 4 HOH H 5 2005 2005 HOH HOH . D 4 HOH H 6 2006 2006 HOH HOH . D 4 HOH H 7 2007 2007 HOH HOH . D 4 HOH H 8 2008 2008 HOH HOH . D 4 HOH H 9 2009 2009 HOH HOH . D 4 HOH H 10 2010 2010 HOH HOH . D 4 HOH H 11 2011 2011 HOH HOH . D 4 HOH H 12 2012 2012 HOH HOH . D 4 HOH H 13 2013 2013 HOH HOH . D 4 HOH H 14 2014 2014 HOH HOH . D 4 HOH H 15 2015 2015 HOH HOH . D 4 HOH H 16 2016 2016 HOH HOH . D 4 HOH H 17 2017 2017 HOH HOH . D 4 HOH H 18 2018 2018 HOH HOH . D 4 HOH H 19 2019 2019 HOH HOH . D 4 HOH H 20 2020 2020 HOH HOH . D 4 HOH H 21 2021 2021 HOH HOH . D 4 HOH H 22 2022 2022 HOH HOH . D 4 HOH H 23 2023 2023 HOH HOH . D 4 HOH H 24 2024 2024 HOH HOH . D 4 HOH H 25 2025 2025 HOH HOH . D 4 HOH H 26 2026 2026 HOH HOH . D 4 HOH H 27 2027 2027 HOH HOH . D 4 HOH H 28 2028 2028 HOH HOH . D 4 HOH H 29 2029 2029 HOH HOH . D 4 HOH H 30 2030 2030 HOH HOH . D 4 HOH H 31 2031 2031 HOH HOH . D 4 HOH H 32 2032 2032 HOH HOH . D 4 HOH H 33 2033 2033 HOH HOH . D 4 HOH H 34 2034 2034 HOH HOH . D 4 HOH H 35 2035 2035 HOH HOH . D 4 HOH H 36 2036 2036 HOH HOH . D 4 HOH H 37 2037 2037 HOH HOH . D 4 HOH H 38 2038 2038 HOH HOH . D 4 HOH H 39 2039 2039 HOH HOH . D 4 HOH H 40 2040 2040 HOH HOH . D 4 HOH H 41 2041 2041 HOH HOH . D 4 HOH H 42 2042 2042 HOH HOH . D 4 HOH H 43 2043 2043 HOH HOH . D 4 HOH H 44 2044 2044 HOH HOH . D 4 HOH H 45 2045 2045 HOH HOH . D 4 HOH H 46 2046 2046 HOH HOH . D 4 HOH H 47 2047 2047 HOH HOH . D 4 HOH H 48 2048 2048 HOH HOH . D 4 HOH H 49 2049 2049 HOH HOH . D 4 HOH H 50 2050 2050 HOH HOH . D 4 HOH H 51 2051 2051 HOH HOH . D 4 HOH H 52 2052 2052 HOH HOH . D 4 HOH H 53 2053 2053 HOH HOH . D 4 HOH H 54 2054 2054 HOH HOH . D 4 HOH H 55 2055 2055 HOH HOH . D 4 HOH H 56 2056 2056 HOH HOH . D 4 HOH H 57 2057 2057 HOH HOH . D 4 HOH H 58 2058 2058 HOH HOH . D 4 HOH H 59 2059 2059 HOH HOH . D 4 HOH H 60 2060 2060 HOH HOH . D 4 HOH H 61 2061 2061 HOH HOH . D 4 HOH H 62 2062 2062 HOH HOH . D 4 HOH H 63 2063 2063 HOH HOH . D 4 HOH H 64 2064 2064 HOH HOH . D 4 HOH H 65 2065 2065 HOH HOH . D 4 HOH H 66 2066 2066 HOH HOH . D 4 HOH H 67 2067 2067 HOH HOH . D 4 HOH H 68 2068 2068 HOH HOH . D 4 HOH H 69 2069 2069 HOH HOH . D 4 HOH H 70 2070 2070 HOH HOH . D 4 HOH H 71 2071 2071 HOH HOH . D 4 HOH H 72 2072 2072 HOH HOH . D 4 HOH H 73 2073 2073 HOH HOH . D 4 HOH H 74 2074 2074 HOH HOH . D 4 HOH H 75 2075 2075 HOH HOH . D 4 HOH H 76 2076 2076 HOH HOH . D 4 HOH H 77 2077 2077 HOH HOH . D 4 HOH H 78 2078 2078 HOH HOH . D 4 HOH H 79 2079 2079 HOH HOH . D 4 HOH H 80 2080 2080 HOH HOH . D 4 HOH H 81 2081 2081 HOH HOH . D 4 HOH H 82 2082 2082 HOH HOH . D 4 HOH H 83 2083 2083 HOH HOH . D 4 HOH H 84 2084 2084 HOH HOH . D 4 HOH H 85 2085 2085 HOH HOH . D 4 HOH H 86 2086 2086 HOH HOH . D 4 HOH H 87 2087 2087 HOH HOH . E 4 HOH L 1 2001 2001 HOH HOH . E 4 HOH L 2 2002 2002 HOH HOH . E 4 HOH L 3 2003 2003 HOH HOH . E 4 HOH L 4 2004 2004 HOH HOH . E 4 HOH L 5 2005 2005 HOH HOH . E 4 HOH L 6 2006 2006 HOH HOH . E 4 HOH L 7 2007 2007 HOH HOH . E 4 HOH L 8 2008 2008 HOH HOH . E 4 HOH L 9 2009 2009 HOH HOH . E 4 HOH L 10 2010 2010 HOH HOH . E 4 HOH L 11 2011 2011 HOH HOH . E 4 HOH L 12 2012 2012 HOH HOH . E 4 HOH L 13 2013 2013 HOH HOH . E 4 HOH L 14 2014 2014 HOH HOH . E 4 HOH L 15 2015 2015 HOH HOH . E 4 HOH L 16 2016 2016 HOH HOH . E 4 HOH L 17 2017 2017 HOH HOH . E 4 HOH L 18 2018 2018 HOH HOH . E 4 HOH L 19 2019 2019 HOH HOH . E 4 HOH L 20 2020 2020 HOH HOH . E 4 HOH L 21 2021 2021 HOH HOH . E 4 HOH L 22 2022 2022 HOH HOH . E 4 HOH L 23 2023 2023 HOH HOH . E 4 HOH L 24 2024 2024 HOH HOH . E 4 HOH L 25 2025 2025 HOH HOH . E 4 HOH L 26 2026 2026 HOH HOH . E 4 HOH L 27 2027 2027 HOH HOH . E 4 HOH L 28 2028 2028 HOH HOH . E 4 HOH L 29 2029 2029 HOH HOH . E 4 HOH L 30 2030 2030 HOH HOH . E 4 HOH L 31 2031 2031 HOH HOH . E 4 HOH L 32 2032 2032 HOH HOH . E 4 HOH L 33 2033 2033 HOH HOH . E 4 HOH L 34 2034 2034 HOH HOH . E 4 HOH L 35 2035 2035 HOH HOH . E 4 HOH L 36 2036 2036 HOH HOH . E 4 HOH L 37 2037 2037 HOH HOH . E 4 HOH L 38 2038 2038 HOH HOH . E 4 HOH L 39 2039 2039 HOH HOH . E 4 HOH L 40 2040 2040 HOH HOH . E 4 HOH L 41 2041 2041 HOH HOH . E 4 HOH L 42 2042 2042 HOH HOH . E 4 HOH L 43 2043 2043 HOH HOH . E 4 HOH L 44 2044 2044 HOH HOH . E 4 HOH L 45 2045 2045 HOH HOH . E 4 HOH L 46 2046 2046 HOH HOH . E 4 HOH L 47 2047 2047 HOH HOH . E 4 HOH L 48 2048 2048 HOH HOH . E 4 HOH L 49 2049 2049 HOH HOH . E 4 HOH L 50 2050 2050 HOH HOH . E 4 HOH L 51 2051 2051 HOH HOH . E 4 HOH L 52 2052 2052 HOH HOH . E 4 HOH L 53 2053 2053 HOH HOH . E 4 HOH L 54 2054 2054 HOH HOH . E 4 HOH L 55 2055 2055 HOH HOH . E 4 HOH L 56 2056 2056 HOH HOH . E 4 HOH L 57 2057 2057 HOH HOH . E 4 HOH L 58 2058 2058 HOH HOH . E 4 HOH L 59 2059 2059 HOH HOH . E 4 HOH L 60 2060 2060 HOH HOH . E 4 HOH L 61 2061 2061 HOH HOH . E 4 HOH L 62 2062 2062 HOH HOH . E 4 HOH L 63 2063 2063 HOH HOH . E 4 HOH L 64 2064 2064 HOH HOH . E 4 HOH L 65 2065 2065 HOH HOH . E 4 HOH L 66 2066 2066 HOH HOH . E 4 HOH L 67 2067 2067 HOH HOH . E 4 HOH L 68 2068 2068 HOH HOH . E 4 HOH L 69 2069 2069 HOH HOH . E 4 HOH L 70 2070 2070 HOH HOH . E 4 HOH L 71 2071 2071 HOH HOH . E 4 HOH L 72 2072 2072 HOH HOH . E 4 HOH L 73 2073 2073 HOH HOH . E 4 HOH L 74 2074 2074 HOH HOH . E 4 HOH L 75 2075 2075 HOH HOH . E 4 HOH L 76 2076 2076 HOH HOH . E 4 HOH L 77 2077 2077 HOH HOH . E 4 HOH L 78 2078 2078 HOH HOH . E 4 HOH L 79 2079 2079 HOH HOH . E 4 HOH L 80 2080 2080 HOH HOH . E 4 HOH L 81 2081 2081 HOH HOH . E 4 HOH L 82 2082 2082 HOH HOH . E 4 HOH L 83 2083 2083 HOH HOH . E 4 HOH L 84 2084 2084 HOH HOH . E 4 HOH L 85 2085 2085 HOH HOH . E 4 HOH L 86 2086 2086 HOH HOH . E 4 HOH L 87 2087 2087 HOH HOH . E 4 HOH L 88 2088 2088 HOH HOH . E 4 HOH L 89 2089 2089 HOH HOH . E 4 HOH L 90 2090 2090 HOH HOH . E 4 HOH L 91 2091 2091 HOH HOH . E 4 HOH L 92 2092 2092 HOH HOH . E 4 HOH L 93 2093 2093 HOH HOH . E 4 HOH L 94 2094 2094 HOH HOH . E 4 HOH L 95 2095 2095 HOH HOH . E 4 HOH L 96 2096 2096 HOH HOH . E 4 HOH L 97 2097 2097 HOH HOH . E 4 HOH L 98 2098 2098 HOH HOH . E 4 HOH L 99 2099 2099 HOH HOH . E 4 HOH L 100 2100 2100 HOH HOH . E 4 HOH L 101 2101 2101 HOH HOH . E 4 HOH L 102 2102 2102 HOH HOH . E 4 HOH L 103 2103 2103 HOH HOH . E 4 HOH L 104 2104 2104 HOH HOH . E 4 HOH L 105 2105 2105 HOH HOH . E 4 HOH L 106 2106 2106 HOH HOH . E 4 HOH L 107 2107 2107 HOH HOH . E 4 HOH L 108 2108 2108 HOH HOH . E 4 HOH L 109 2109 2109 HOH HOH . E 4 HOH L 110 2110 2110 HOH HOH . E 4 HOH L 111 2111 2111 HOH HOH . E 4 HOH L 112 2112 2112 HOH HOH . E 4 HOH L 113 2113 2113 HOH HOH . E 4 HOH L 114 2114 2114 HOH HOH . E 4 HOH L 115 2115 2115 HOH HOH . E 4 HOH L 116 2116 2116 HOH HOH . E 4 HOH L 117 2117 2117 HOH HOH . E 4 HOH L 118 2118 2118 HOH HOH . E 4 HOH L 119 2119 2119 HOH HOH . E 4 HOH L 120 2120 2120 HOH HOH . E 4 HOH L 121 2121 2121 HOH HOH . E 4 HOH L 122 2122 2122 HOH HOH . E 4 HOH L 123 2123 2123 HOH HOH . E 4 HOH L 124 2124 2124 HOH HOH . E 4 HOH L 125 2125 2125 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 GOL . . . C 3 10.26 16.043 8.801 1 45.68 ? C1 GOL 1214 L 1 HETATM 2 O O1 GOL . . . C 3 11.12 15.255 9.644 1 46.81 ? O1 GOL 1214 L 1 HETATM 3 C C2 GOL . . . C 3 8.81 15.817 9.218 1 47.52 ? C2 GOL 1214 L 1 HETATM 4 O O2 GOL . . . C 3 8.511 14.428 9.054 1 51.79 ? O2 GOL 1214 L 1 HETATM 5 C C3 GOL . . . C 3 7.783 16.627 8.418 1 41.78 ? C3 GOL 1214 L 1 HETATM 6 O O3 GOL . . . C 3 8.311 17.485 7.397 1 35.4 ? O3 GOL 1214 L 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #