data_3TXD # _model_server_result.job_id D6O2d4Vpr6B8VFv7PGA3Xg _model_server_result.datetime_utc '2024-10-12 15:30:15' _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 3txd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":139}' # _entry.id 3TXD # _exptl.entry_id 3TXD _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 13 _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 3TXD _cell.length_a 78.87 _cell.length_b 78.87 _cell.length_c 36.98 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TXD _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 ? 4 K N N ? 4 L N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N ? 4 R N N ? 4 T N N ? 4 U N N ? 4 V N N ? 4 W N N ? 4 X N N ? 4 Y 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 disulf ? disulf1 A SG CYS 6 A CYS 6 1_555 A SG CYS 127 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A O SER 60 A SER 60 1_555 J NA NA . A NA 1138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc2 A O CYS 64 A CYS 64 1_555 J NA NA . A NA 1138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc3 A OD1 ASP 66 A ASP 66 1_555 M NA NA . A NA 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.073 ? metalc ? metalc4 A OG SER 72 A SER 72 1_555 J NA NA . A NA 1138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc5 A O ARG 73 A ARG 73 1_555 J NA NA . A NA 1138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc6 L O3 GOL . A GOL 130 1_555 M NA NA . A NA 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? metalc ? metalc7 L O3 GOL . A GOL 130 1_555 J NA NA . A NA 1138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? # _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 3TXD _atom_sites.fract_transf_matrix[1][1] 0.012679 _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] 0.012679 _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] 0.027042 _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 CL A 1 1130 1130 CL CL . C 2 CL A 1 1131 1131 CL CL . D 2 CL A 1 1132 1132 CL CL . E 2 CL A 1 1133 1133 CL CL . F 2 CL A 1 1134 1134 CL CL . G 2 CL A 1 1135 1135 CL CL . H 2 CL A 1 1136 1136 CL CL . I 2 CL A 1 1137 1137 CL CL . J 3 NA A 1 1138 1138 NA NA . K 4 GOL A 1 801 801 GOL GOL . L 4 GOL A 1 130 801 GOL GOL . M 3 NA A 1 131 1 NA NA . N 4 GOL A 1 132 801 GOL GOL . O 4 GOL A 1 133 801 GOL GOL . P 4 GOL A 1 134 801 GOL GOL . Q 4 GOL A 1 135 801 GOL GOL . R 4 GOL A 1 136 801 GOL GOL . S 3 NA A 1 137 1 NA NA . T 4 GOL A 1 138 801 GOL GOL . U 4 GOL A 1 139 801 GOL GOL . V 4 GOL A 1 140 801 GOL GOL . W 4 GOL A 1 141 801 GOL GOL . X 4 GOL A 1 142 801 GOL GOL . Y 4 GOL A 1 143 801 GOL GOL . Z 5 HOH A 1 2001 2001 HOH HOH . Z 5 HOH A 2 2002 2002 HOH HOH . Z 5 HOH A 3 2003 2003 HOH HOH . Z 5 HOH A 4 2004 2004 HOH HOH . Z 5 HOH A 5 2005 2005 HOH HOH . Z 5 HOH A 6 2006 1 HOH HOH . Z 5 HOH A 7 2008 2008 HOH HOH . Z 5 HOH A 8 2009 2009 HOH HOH . Z 5 HOH A 9 2010 2010 HOH HOH . Z 5 HOH A 10 2012 2012 HOH HOH . Z 5 HOH A 11 2013 2013 HOH HOH . Z 5 HOH A 12 2014 2014 HOH HOH . Z 5 HOH A 13 2015 2015 HOH HOH . Z 5 HOH A 14 2019 2019 HOH HOH . Z 5 HOH A 15 2021 2021 HOH HOH . Z 5 HOH A 16 2024 2024 HOH HOH . Z 5 HOH A 17 2025 2025 HOH HOH . Z 5 HOH A 18 2026 2026 HOH HOH . Z 5 HOH A 19 2027 2027 HOH HOH . Z 5 HOH A 20 2028 2028 HOH HOH . Z 5 HOH A 21 2030 2030 HOH HOH . Z 5 HOH A 22 2031 2031 HOH HOH . Z 5 HOH A 23 2032 2032 HOH HOH . Z 5 HOH A 24 2033 2033 HOH HOH . Z 5 HOH A 25 2036 2036 HOH HOH . Z 5 HOH A 26 2037 2037 HOH HOH . Z 5 HOH A 27 2038 2038 HOH HOH . Z 5 HOH A 28 2039 2039 HOH HOH . Z 5 HOH A 29 2040 2040 HOH HOH . Z 5 HOH A 30 2042 2042 HOH HOH . Z 5 HOH A 31 2043 2043 HOH HOH . Z 5 HOH A 32 2044 2044 HOH HOH . Z 5 HOH A 33 2045 2045 HOH HOH . Z 5 HOH A 34 2046 2046 HOH HOH . Z 5 HOH A 35 2047 2047 HOH HOH . Z 5 HOH A 36 2050 2050 HOH HOH . Z 5 HOH A 37 2051 2051 HOH HOH . Z 5 HOH A 38 2053 2053 HOH HOH . Z 5 HOH A 39 2056 2056 HOH HOH . Z 5 HOH A 40 2057 2057 HOH HOH . Z 5 HOH A 41 2058 2058 HOH HOH . Z 5 HOH A 42 2064 2064 HOH HOH . Z 5 HOH A 43 2065 2065 HOH HOH . Z 5 HOH A 44 2066 2066 HOH HOH . Z 5 HOH A 45 2067 2067 HOH HOH . Z 5 HOH A 46 2068 2068 HOH HOH . Z 5 HOH A 47 2071 2071 HOH HOH . Z 5 HOH A 48 2073 2073 HOH HOH . Z 5 HOH A 49 2074 2074 HOH HOH . Z 5 HOH A 50 2075 2075 HOH HOH . Z 5 HOH A 51 2076 2076 HOH HOH . Z 5 HOH A 52 2078 2078 HOH HOH . Z 5 HOH A 53 2079 2079 HOH HOH . Z 5 HOH A 54 2081 2081 HOH HOH . Z 5 HOH A 55 2083 2083 HOH HOH . Z 5 HOH A 56 2084 2084 HOH HOH . Z 5 HOH A 57 2085 2085 HOH HOH . Z 5 HOH A 58 2086 2086 HOH HOH . Z 5 HOH A 59 2087 2087 HOH HOH . Z 5 HOH A 60 2088 2088 HOH HOH . Z 5 HOH A 61 2090 2090 HOH HOH . Z 5 HOH A 62 2091 2091 HOH HOH . Z 5 HOH A 63 2092 2092 HOH HOH . Z 5 HOH A 64 2093 2093 HOH HOH . Z 5 HOH A 65 2094 2094 HOH HOH . Z 5 HOH A 66 2095 2095 HOH HOH . Z 5 HOH A 67 2096 2096 HOH HOH . Z 5 HOH A 68 2097 2097 HOH HOH . Z 5 HOH A 69 2098 2098 HOH HOH . Z 5 HOH A 70 2099 2099 HOH HOH . Z 5 HOH A 71 2100 2100 HOH HOH . Z 5 HOH A 72 2101 2101 HOH HOH . Z 5 HOH A 73 2102 2102 HOH HOH . Z 5 HOH A 74 2103 2103 HOH HOH . Z 5 HOH A 75 2104 2104 HOH HOH . Z 5 HOH A 76 2105 2105 HOH HOH . Z 5 HOH A 77 2106 2106 HOH HOH . Z 5 HOH A 78 2107 2107 HOH HOH . Z 5 HOH A 79 2108 2108 HOH HOH . Z 5 HOH A 80 2109 2109 HOH HOH . Z 5 HOH A 81 2110 2110 HOH HOH . Z 5 HOH A 82 2112 2112 HOH HOH . Z 5 HOH A 83 2113 2113 HOH HOH . Z 5 HOH A 84 2114 2114 HOH HOH . Z 5 HOH A 85 2115 2115 HOH HOH . Z 5 HOH A 86 2116 2116 HOH HOH . Z 5 HOH A 87 2117 2117 HOH HOH . Z 5 HOH A 88 2118 2118 HOH HOH . Z 5 HOH A 89 2119 2119 HOH HOH . Z 5 HOH A 90 2120 2120 HOH HOH . Z 5 HOH A 91 2121 2121 HOH HOH . Z 5 HOH A 92 2122 2122 HOH HOH . Z 5 HOH A 93 2123 2123 HOH HOH . Z 5 HOH A 94 2124 2124 HOH HOH . Z 5 HOH A 95 2125 2125 HOH HOH . Z 5 HOH A 96 2127 2127 HOH HOH . Z 5 HOH A 97 2128 2128 HOH HOH . Z 5 HOH A 98 2130 2130 HOH HOH . Z 5 HOH A 99 2133 2133 HOH HOH . Z 5 HOH A 100 2134 2134 HOH HOH . Z 5 HOH A 101 2135 2135 HOH HOH . Z 5 HOH A 102 2136 2136 HOH HOH . Z 5 HOH A 103 2137 2137 HOH HOH . Z 5 HOH A 104 2138 2138 HOH HOH . Z 5 HOH A 105 2139 2139 HOH HOH . Z 5 HOH A 106 2140 2140 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 . . . U 4 -9.646 -6.961 3.888 1 92.28 ? C1 GOL 139 A 1 HETATM 2 O O1 GOL . . . U 4 -8.46 -6.42 4.443 1 92.05 ? O1 GOL 139 A 1 HETATM 3 C C2 GOL . . . U 4 -10.916 -6.14 4.181 1 92.65 ? C2 GOL 139 A 1 HETATM 4 O O2 GOL . . . U 4 -10.909 -4.846 3.602 1 91.28 ? O2 GOL 139 A 1 HETATM 5 C C3 GOL . . . U 4 -11.341 -6.144 5.654 1 92.47 ? C3 GOL 139 A 1 HETATM 6 O O3 GOL . . . U 4 -12.727 -6.409 5.76 1 91.87 ? O3 GOL 139 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 6 #