data_3VGH # _model_server_result.job_id mKpub7NfS-TlL305DoQg1Q _model_server_result.datetime_utc '2025-03-06 07:57:58' _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 3vgh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1101}' # _entry.id 3VGH # _exptl.entry_id 3VGH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _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 3VGH _cell.length_a 78.801 _cell.length_b 78.801 _cell.length_c 282.704 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VGH _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 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' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 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 ? 4 D N N ? 4 E N N ? 4 F N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 1 2 GLC GLC C1 O1 . O4 HO4 . sing 2 ? 2 2 3 GLC GLC C1 O1 . O4 HO4 . sing 3 ? 2 3 4 GLC GLC C1 O1 . O4 HO4 . sing 4 ? 2 5 4 GLC GLC C1 O1 . O1 HO1 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC B 602 GLC 2 n B GLC 2 B 2 GLC B 603 GLC 2 n B GLC 3 B 3 GLC B 604 GLC 2 n B GLC 4 B 4 GLC B 605 GLC 2 n B GLC 5 B 5 GLC B 606 GLC # 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 298 A CYS 298 1_555 A SG CYS 298 A CYS 298 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 367 A CYS 367 1_555 A SG CYS 491 A CYS 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? covale ? covale1 B C1 GLC . B GLC 1 1_555 B O4 GLC . B GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 B C1 GLC . B GLC 2 1_555 B O4 GLC . B GLC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 B C1 GLC . B GLC 3 1_555 B O4 GLC . B GLC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 B O1 GLC . B GLC 4 1_555 B C1 GLC . B GLC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 170 n n C1 C2 GOL sing 171 n n C1 H11 GOL sing 172 n n C1 H12 GOL sing 173 n n O1 HO1 GOL sing 174 n n C2 O2 GOL sing 175 n n C2 C3 GOL sing 176 n n C2 H2 GOL sing 177 n n O2 HO2 GOL sing 178 n n C3 O3 GOL sing 179 n n C3 H31 GOL sing 180 n n C3 H32 GOL sing 181 n n O3 HO3 GOL sing 182 n n # _atom_sites.entry_id 3VGH _atom_sites.fract_transf_matrix[1][1] 0.01269 _atom_sites.fract_transf_matrix[1][2] 0.007327 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014653 _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] 0.003537 _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 FLC A 1 1001 1 FLC FLC . D 4 GOL A 1 1101 1 GOL GOL . E 4 GOL A 1 1102 2 GOL GOL . F 4 GOL A 1 1103 3 GOL GOL . G 5 HOH A 1 2001 1 HOH HOH . G 5 HOH A 2 2002 2 HOH HOH . G 5 HOH A 3 2003 3 HOH HOH . G 5 HOH A 4 2004 4 HOH HOH . G 5 HOH A 5 2005 5 HOH HOH . G 5 HOH A 6 2006 6 HOH HOH . G 5 HOH A 7 2007 7 HOH HOH . G 5 HOH A 8 2008 8 HOH HOH . G 5 HOH A 9 2009 9 HOH HOH . G 5 HOH A 10 2010 10 HOH HOH . G 5 HOH A 11 2011 11 HOH HOH . G 5 HOH A 12 2012 12 HOH HOH . G 5 HOH A 13 2013 13 HOH HOH . G 5 HOH A 14 2014 14 HOH HOH . G 5 HOH A 15 2015 15 HOH HOH . G 5 HOH A 16 2016 16 HOH HOH . G 5 HOH A 17 2017 17 HOH HOH . G 5 HOH A 18 2018 18 HOH HOH . G 5 HOH A 19 2019 19 HOH HOH . G 5 HOH A 20 2020 20 HOH HOH . G 5 HOH A 21 2021 21 HOH HOH . G 5 HOH A 22 2022 22 HOH HOH . G 5 HOH A 23 2023 23 HOH HOH . G 5 HOH A 24 2024 24 HOH HOH . G 5 HOH A 25 2025 25 HOH HOH . G 5 HOH A 26 2026 26 HOH HOH . G 5 HOH A 27 2027 27 HOH HOH . G 5 HOH A 28 2028 28 HOH HOH . G 5 HOH A 29 2029 29 HOH HOH . G 5 HOH A 30 2030 30 HOH HOH . G 5 HOH A 31 2031 31 HOH HOH . G 5 HOH A 32 2032 32 HOH HOH . G 5 HOH A 33 2033 33 HOH HOH . G 5 HOH A 34 2034 34 HOH HOH . G 5 HOH A 35 2035 35 HOH HOH . G 5 HOH A 36 2036 36 HOH HOH . G 5 HOH A 37 2037 37 HOH HOH . G 5 HOH A 38 2038 38 HOH HOH . G 5 HOH A 39 2039 39 HOH HOH . G 5 HOH A 40 2040 40 HOH HOH . G 5 HOH A 41 2041 41 HOH HOH . G 5 HOH A 42 2042 42 HOH HOH . G 5 HOH A 43 2043 43 HOH HOH . G 5 HOH A 44 2044 44 HOH HOH . G 5 HOH A 45 2045 45 HOH HOH . G 5 HOH A 46 2046 46 HOH HOH . G 5 HOH A 47 2047 47 HOH HOH . G 5 HOH A 48 2048 48 HOH HOH . G 5 HOH A 49 2049 49 HOH HOH . G 5 HOH A 50 2050 50 HOH HOH . G 5 HOH A 51 2051 51 HOH HOH . G 5 HOH A 52 2052 52 HOH HOH . G 5 HOH A 53 2053 53 HOH HOH . G 5 HOH A 54 2054 54 HOH HOH . G 5 HOH A 55 2055 55 HOH HOH . G 5 HOH A 56 2056 56 HOH HOH . G 5 HOH A 57 2057 57 HOH HOH . G 5 HOH A 58 2058 58 HOH HOH . G 5 HOH A 59 2059 59 HOH HOH . G 5 HOH A 60 2060 60 HOH HOH . G 5 HOH A 61 2061 61 HOH HOH . G 5 HOH A 62 2062 62 HOH HOH . G 5 HOH A 63 2063 63 HOH HOH . G 5 HOH A 64 2064 64 HOH HOH . G 5 HOH A 65 2065 65 HOH HOH . G 5 HOH A 66 2066 66 HOH HOH . G 5 HOH A 67 2067 67 HOH HOH . G 5 HOH A 68 2068 68 HOH HOH . G 5 HOH A 69 2069 69 HOH HOH . G 5 HOH A 70 2070 70 HOH HOH . G 5 HOH A 71 2071 71 HOH HOH . G 5 HOH A 72 2072 72 HOH HOH . G 5 HOH A 73 2073 73 HOH HOH . G 5 HOH A 74 2074 74 HOH HOH . G 5 HOH A 75 2075 75 HOH HOH . G 5 HOH A 76 2076 76 HOH HOH . G 5 HOH A 77 2077 77 HOH HOH . G 5 HOH A 78 2078 78 HOH HOH . G 5 HOH A 79 2079 79 HOH HOH . G 5 HOH A 80 2080 80 HOH HOH . G 5 HOH A 81 2081 81 HOH HOH . G 5 HOH A 82 2082 82 HOH HOH . G 5 HOH A 83 2083 83 HOH HOH . G 5 HOH A 84 2084 84 HOH HOH . G 5 HOH A 85 2085 85 HOH HOH . G 5 HOH A 86 2086 86 HOH HOH . G 5 HOH A 87 2087 87 HOH HOH . G 5 HOH A 88 2088 88 HOH HOH . G 5 HOH A 89 2089 89 HOH HOH . G 5 HOH A 90 2090 90 HOH HOH . G 5 HOH A 91 2091 91 HOH HOH . G 5 HOH A 92 2092 92 HOH HOH . G 5 HOH A 93 2093 93 HOH HOH . G 5 HOH A 94 2094 94 HOH HOH . G 5 HOH A 95 2095 95 HOH HOH . G 5 HOH A 96 2096 96 HOH HOH . G 5 HOH A 97 2097 97 HOH HOH . G 5 HOH A 98 2098 98 HOH HOH . G 5 HOH A 99 2099 99 HOH HOH . G 5 HOH A 100 2100 100 HOH HOH . G 5 HOH A 101 2101 101 HOH HOH . G 5 HOH A 102 2102 102 HOH HOH . G 5 HOH A 103 2103 103 HOH HOH . G 5 HOH A 104 2104 104 HOH HOH . G 5 HOH A 105 2105 105 HOH HOH . G 5 HOH A 106 2106 106 HOH HOH . G 5 HOH A 107 2107 107 HOH HOH . G 5 HOH A 108 2108 108 HOH HOH . G 5 HOH A 109 2109 109 HOH HOH . G 5 HOH A 110 2110 110 HOH HOH . G 5 HOH A 111 2111 111 HOH HOH . G 5 HOH A 112 2112 112 HOH HOH . G 5 HOH A 113 2113 113 HOH HOH . G 5 HOH A 114 2114 114 HOH HOH . G 5 HOH A 115 2115 115 HOH HOH . G 5 HOH A 116 2116 116 HOH HOH . G 5 HOH A 117 2117 117 HOH HOH . G 5 HOH A 118 2118 118 HOH HOH . G 5 HOH A 119 2119 119 HOH HOH . G 5 HOH A 120 2120 120 HOH HOH . G 5 HOH A 121 2121 121 HOH HOH . G 5 HOH A 122 2122 122 HOH HOH . G 5 HOH A 123 2123 123 HOH HOH . G 5 HOH A 124 2124 124 HOH HOH . G 5 HOH A 125 2125 125 HOH HOH . G 5 HOH A 126 2126 126 HOH HOH . G 5 HOH A 127 2127 127 HOH HOH . G 5 HOH A 128 2128 128 HOH HOH . G 5 HOH A 129 2129 129 HOH HOH . G 5 HOH A 130 2130 130 HOH HOH . G 5 HOH A 131 2131 131 HOH HOH . G 5 HOH A 132 2132 132 HOH HOH . G 5 HOH A 133 2133 133 HOH HOH . G 5 HOH A 134 2134 134 HOH HOH . G 5 HOH A 135 2135 135 HOH HOH . G 5 HOH A 136 2136 136 HOH HOH . G 5 HOH A 137 2137 137 HOH HOH . G 5 HOH A 138 2138 138 HOH HOH . G 5 HOH A 139 2139 139 HOH HOH . G 5 HOH A 140 2140 140 HOH HOH . G 5 HOH A 141 2141 141 HOH HOH . G 5 HOH A 142 2142 142 HOH HOH . G 5 HOH A 143 2143 143 HOH HOH . G 5 HOH A 144 2144 144 HOH HOH . G 5 HOH A 145 2145 145 HOH HOH . G 5 HOH A 146 2146 146 HOH HOH . G 5 HOH A 147 2147 147 HOH HOH . G 5 HOH A 148 2148 148 HOH HOH . G 5 HOH A 149 2149 149 HOH HOH . G 5 HOH A 150 2150 150 HOH HOH . G 5 HOH A 151 2151 151 HOH HOH . G 5 HOH A 152 2152 152 HOH HOH . G 5 HOH A 153 2153 153 HOH HOH . G 5 HOH A 154 2154 154 HOH HOH . G 5 HOH A 155 2155 155 HOH HOH . G 5 HOH A 156 2156 156 HOH HOH . G 5 HOH A 157 2157 157 HOH HOH . G 5 HOH A 158 2158 158 HOH HOH . G 5 HOH A 159 2159 159 HOH HOH . G 5 HOH A 160 2160 160 HOH HOH . G 5 HOH A 161 2161 161 HOH HOH . G 5 HOH A 162 2162 162 HOH HOH . G 5 HOH A 163 2163 163 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 . . . D 4 22.336 47.888 14.553 1 74.89 ? C1 GOL 1101 A 1 HETATM 2 O O1 GOL . . . D 4 23.124 47.376 15.605 1 73.65 ? O1 GOL 1101 A 1 HETATM 3 C C2 GOL . . . D 4 20.987 47.176 14.498 1 75.38 ? C2 GOL 1101 A 1 HETATM 4 O O2 GOL . . . D 4 21.176 45.803 14.201 1 75.39 ? O2 GOL 1101 A 1 HETATM 5 C C3 GOL . . . D 4 20.145 47.844 13.412 1 75.58 ? C3 GOL 1101 A 1 HETATM 6 O O3 GOL . . . D 4 18.875 47.233 13.318 1 75.46 ? O3 GOL 1101 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #