data_3ZG6 # _model_server_result.job_id ZcRgY0E2mi91legvF22sXA _model_server_result.datetime_utc '2024-11-18 13:23:40' _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 3zg6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1296}' # _entry.id 3ZG6 # _exptl.entry_id 3ZG6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _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 120 _cell.entry_id 3ZG6 _cell.length_a 104.891 _cell.length_b 104.891 _cell.length_c 231.492 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZG6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 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 _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 4 _struct_asym.id D _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 metalc ? metalc1 C ZN ZN . A ZN 1295 1_555 A SG CYS 141 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc2 C ZN ZN . A ZN 1295 1_555 A SG CYS 177 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc3 C ZN ZN . A ZN 1295 1_555 A SG CYS 166 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc4 C ZN ZN . A ZN 1295 1_555 A SG CYS 144 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? covale ? covale1 B N MYK 6 F MYK 9 1_555 B C ARG 5 F ARG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 B C MYK 6 F MYK 9 1_555 B N SER 7 F SER 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3ZG6 _atom_sites.fract_transf_matrix[1][1] 0.009534 _atom_sites.fract_transf_matrix[1][2] 0.005504 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011009 _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] 0.00432 _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 ZN A 1 1295 1295 ZN ZN . D 4 APR A 1 1296 1296 APR APR . E 5 GOL A 1 1298 1298 GOL GOL . F 5 GOL A 1 1299 1299 GOL GOL . G 6 HOH A 1 2001 2001 HOH HOH . G 6 HOH A 2 2002 2002 HOH HOH . G 6 HOH A 3 2003 2003 HOH HOH . G 6 HOH A 4 2004 2004 HOH HOH . G 6 HOH A 5 2005 2005 HOH HOH . G 6 HOH A 6 2006 2006 HOH HOH . G 6 HOH A 7 2007 2007 HOH HOH . G 6 HOH A 8 2008 2008 HOH HOH . G 6 HOH A 9 2009 2009 HOH HOH . G 6 HOH A 10 2010 2010 HOH HOH . G 6 HOH A 11 2011 2011 HOH HOH . G 6 HOH A 12 2012 2012 HOH HOH . G 6 HOH A 13 2013 2013 HOH HOH . G 6 HOH A 14 2014 2014 HOH HOH . G 6 HOH A 15 2015 2015 HOH HOH . G 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH A 17 2017 2017 HOH HOH . G 6 HOH A 18 2018 2018 HOH HOH . G 6 HOH A 19 2019 2019 HOH HOH . G 6 HOH A 20 2020 2020 HOH HOH . G 6 HOH A 21 2021 2021 HOH HOH . G 6 HOH A 22 2022 2022 HOH HOH . G 6 HOH A 23 2023 2023 HOH HOH . G 6 HOH A 24 2024 2024 HOH HOH . G 6 HOH A 25 2025 2025 HOH HOH . G 6 HOH A 26 2026 2026 HOH HOH . G 6 HOH A 27 2027 2027 HOH HOH . G 6 HOH A 28 2028 2028 HOH HOH . G 6 HOH A 29 2029 2029 HOH HOH . G 6 HOH A 30 2030 2030 HOH HOH . G 6 HOH A 31 2031 2031 HOH HOH . G 6 HOH A 32 2032 2032 HOH HOH . G 6 HOH A 33 2033 2033 HOH HOH . G 6 HOH A 34 2034 2034 HOH HOH . G 6 HOH A 35 2035 2035 HOH HOH . G 6 HOH A 36 2036 2036 HOH HOH . G 6 HOH A 37 2037 2037 HOH HOH . G 6 HOH A 38 2038 2038 HOH HOH . G 6 HOH A 39 2039 2039 HOH HOH . G 6 HOH A 40 2040 2040 HOH HOH . G 6 HOH A 41 2041 2041 HOH HOH . G 6 HOH A 42 2042 2042 HOH HOH . G 6 HOH A 43 2043 2043 HOH HOH . G 6 HOH A 44 2044 2044 HOH HOH . G 6 HOH A 45 2045 2045 HOH HOH . G 6 HOH A 46 2046 2046 HOH HOH . G 6 HOH A 47 2047 2047 HOH HOH . G 6 HOH A 48 2048 2048 HOH HOH . G 6 HOH A 49 2049 2049 HOH HOH . G 6 HOH A 50 2050 2050 HOH HOH . G 6 HOH A 51 2051 2051 HOH HOH . G 6 HOH A 52 2052 2052 HOH HOH . G 6 HOH A 53 2053 2053 HOH HOH . G 6 HOH A 54 2054 2054 HOH HOH . G 6 HOH A 55 2055 2055 HOH HOH . G 6 HOH A 56 2056 2056 HOH HOH . G 6 HOH A 57 2057 2057 HOH HOH . G 6 HOH A 58 2058 2058 HOH HOH . G 6 HOH A 59 2059 2059 HOH HOH . G 6 HOH A 60 2060 2060 HOH HOH . G 6 HOH A 61 2061 2061 HOH HOH . G 6 HOH A 62 2062 2062 HOH HOH . G 6 HOH A 63 2063 2063 HOH HOH . G 6 HOH A 64 2064 2064 HOH HOH . G 6 HOH A 65 2065 2065 HOH HOH . G 6 HOH A 66 2066 2066 HOH HOH . G 6 HOH A 67 2067 2067 HOH HOH . G 6 HOH A 68 2068 2068 HOH HOH . G 6 HOH A 69 2069 2069 HOH HOH . G 6 HOH A 70 2070 2070 HOH HOH . G 6 HOH A 71 2071 2071 HOH HOH . G 6 HOH A 72 2072 2072 HOH HOH . G 6 HOH A 73 2073 2073 HOH HOH . G 6 HOH A 74 2074 2074 HOH HOH . G 6 HOH A 75 2075 2075 HOH HOH . G 6 HOH A 76 2076 2076 HOH HOH . G 6 HOH A 77 2077 2077 HOH HOH . G 6 HOH A 78 2078 2078 HOH HOH . G 6 HOH A 79 2079 2079 HOH HOH . G 6 HOH A 80 2080 2080 HOH HOH . G 6 HOH A 81 2081 2081 HOH HOH . G 6 HOH A 82 2082 2082 HOH HOH . G 6 HOH A 83 2083 2083 HOH HOH . G 6 HOH A 84 2084 2084 HOH HOH . G 6 HOH A 85 2085 2085 HOH HOH . G 6 HOH A 86 2086 2086 HOH HOH . G 6 HOH A 87 2087 2087 HOH HOH . G 6 HOH A 88 2088 2088 HOH HOH . G 6 HOH A 89 2089 2089 HOH HOH . G 6 HOH A 90 2090 2090 HOH HOH . G 6 HOH A 91 2091 2091 HOH HOH . G 6 HOH A 92 2092 2092 HOH HOH . G 6 HOH A 93 2093 2093 HOH HOH . G 6 HOH A 94 2094 2094 HOH HOH . G 6 HOH A 95 2095 2095 HOH HOH . G 6 HOH A 96 2096 2096 HOH HOH . G 6 HOH A 97 2097 2097 HOH HOH . G 6 HOH A 98 2098 2098 HOH HOH . G 6 HOH A 99 2099 2099 HOH HOH . G 6 HOH A 100 2100 2100 HOH HOH . G 6 HOH A 101 2101 2101 HOH HOH . G 6 HOH A 102 2102 2102 HOH HOH . G 6 HOH A 103 2103 2103 HOH HOH . G 6 HOH A 104 2104 2104 HOH HOH . G 6 HOH A 105 2105 2105 HOH HOH . G 6 HOH A 106 2106 2106 HOH HOH . G 6 HOH A 107 2107 2107 HOH HOH . G 6 HOH A 108 2108 2108 HOH HOH . G 6 HOH A 109 2109 2109 HOH HOH . G 6 HOH A 110 2110 2110 HOH HOH . G 6 HOH A 111 2111 2111 HOH HOH . G 6 HOH A 112 2112 2112 HOH HOH . G 6 HOH A 113 2113 2113 HOH HOH . G 6 HOH A 114 2114 2114 HOH HOH . G 6 HOH A 115 2115 2115 HOH HOH . G 6 HOH A 116 2116 2116 HOH HOH . G 6 HOH A 117 2117 2117 HOH HOH . G 6 HOH A 118 2118 2118 HOH HOH . G 6 HOH A 119 2119 2119 HOH HOH . G 6 HOH A 120 2120 2120 HOH HOH . G 6 HOH A 121 2121 2121 HOH HOH . G 6 HOH A 122 2122 2122 HOH HOH . G 6 HOH A 123 2123 2123 HOH HOH . G 6 HOH A 124 2124 2124 HOH HOH . G 6 HOH A 125 2125 2125 HOH HOH . G 6 HOH A 126 2126 2126 HOH HOH . G 6 HOH A 127 2127 2127 HOH HOH . G 6 HOH A 128 2128 2128 HOH HOH . G 6 HOH A 129 2129 2129 HOH HOH . G 6 HOH A 130 2130 2130 HOH HOH . G 6 HOH A 131 2131 2131 HOH HOH . G 6 HOH A 132 2132 2132 HOH HOH . G 6 HOH A 133 2133 2133 HOH HOH . G 6 HOH A 134 2134 2134 HOH HOH . G 6 HOH A 135 2135 2135 HOH HOH . G 6 HOH A 136 2136 2136 HOH HOH . G 6 HOH A 137 2137 2137 HOH HOH . G 6 HOH A 138 2138 2138 HOH HOH . G 6 HOH A 139 2139 2139 HOH HOH . G 6 HOH A 140 2140 2140 HOH HOH . G 6 HOH A 141 2141 2141 HOH HOH . G 6 HOH A 142 2142 2142 HOH HOH . G 6 HOH A 143 2143 2143 HOH HOH . G 6 HOH A 144 2144 2144 HOH HOH . G 6 HOH A 145 2145 2145 HOH HOH . G 6 HOH A 146 2146 2146 HOH HOH . H 6 HOH F 1 2001 2001 HOH HOH . H 6 HOH F 2 2002 2002 HOH HOH . H 6 HOH F 3 2003 2003 HOH HOH . H 6 HOH F 4 2004 2004 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 N N1 APR . . . D 4 26.985 -20.36 26.388 1 38.45 ? N1 APR 1296 A 1 HETATM 2 C C2 APR . . . D 4 28.044 -19.86 25.666 1 34.56 ? C2 APR 1296 A 1 HETATM 3 N N3 APR . . . D 4 29.214 -20.521 25.683 1 38.99 ? N3 APR 1296 A 1 HETATM 4 C C4 APR . . . D 4 29.344 -21.691 26.379 1 35.79 ? C4 APR 1296 A 1 HETATM 5 C C5 APR . . . D 4 28.245 -22.195 27.145 1 36.46 ? C5 APR 1296 A 1 HETATM 6 C C6 APR . . . D 4 26.997 -21.432 27.133 1 38.7 ? C6 APR 1296 A 1 HETATM 7 N N6 APR . . . D 4 25.898 -21.86 27.831 1 41.87 ? N6 APR 1296 A 1 HETATM 8 N N7 APR . . . D 4 28.637 -23.327 27.73 1 37.62 ? N7 APR 1296 A 1 HETATM 9 C C8 APR . . . D 4 29.936 -23.554 27.413 1 35.51 ? C8 APR 1296 A 1 HETATM 10 N N9 APR . . . D 4 30.311 -22.535 26.598 1 37.7 ? N9 APR 1296 A 1 HETATM 11 C C1' APR . . . D 4 31.624 -22.48 25.913 1 37.85 ? C1' APR 1296 A 1 HETATM 12 C C2' APR . . . D 4 32.804 -22.999 26.712 1 36.88 ? C2' APR 1296 A 1 HETATM 13 O O2' APR . . . D 4 33.327 -21.739 27.219 1 37.61 ? O2' APR 1296 A 1 HETATM 14 C C3' APR . . . D 4 33.704 -23.633 25.625 1 35.03 ? C3' APR 1296 A 1 HETATM 15 O O3' APR . . . D 4 34.705 -22.715 25.15 1 32.61 ? O3' APR 1296 A 1 HETATM 16 O O4' APR . . . D 4 31.512 -23.44 24.823 1 35.26 ? O4' APR 1296 A 1 HETATM 17 C C4' APR . . . D 4 32.829 -23.857 24.38 1 30.26 ? C4' APR 1296 A 1 HETATM 18 C C5' APR . . . D 4 32.919 -25.357 24.063 1 31.09 ? C5' APR 1296 A 1 HETATM 19 O O5' APR . . . D 4 34.233 -25.601 23.538 1 31.25 ? O5' APR 1296 A 1 HETATM 20 P PA APR . . . D 4 34.845 -27.011 23.665 1 30.78 ? PA APR 1296 A 1 HETATM 21 O O1A APR . . . D 4 34.515 -27.647 24.987 1 31.32 ? O1A APR 1296 A 1 HETATM 22 O O2A APR . . . D 4 36.239 -26.894 23.129 1 29.95 ? O2A APR 1296 A 1 HETATM 23 O O3A APR . . . D 4 33.885 -27.909 22.719 1 32.07 ? O3A APR 1296 A 1 HETATM 24 P PB APR . . . D 4 33.95 -27.856 21.109 1 32.23 ? PB APR 1296 A 1 HETATM 25 O O1B APR . . . D 4 34.528 -26.623 20.532 1 31.66 ? O1B APR 1296 A 1 HETATM 26 O O2B APR . . . D 4 32.595 -28.309 20.598 1 30.9 ? O2B APR 1296 A 1 HETATM 27 O O5D APR . . . D 4 34.963 -29.064 20.906 1 33.04 ? O5D APR 1296 A 1 HETATM 28 C C5D APR . . . D 4 35.337 -29.487 19.58 1 32.48 ? C5D APR 1296 A 1 HETATM 29 O O4D APR . . . D 4 36.668 -31.186 20.679 1 35.78 ? O4D APR 1296 A 1 HETATM 30 O O1D APR . . . D 4 37.465 -33.293 21.704 1 35.54 ? O1D APR 1296 A 1 HETATM 31 C C1D APR . . . D 4 36.583 -32.572 20.914 1 32.51 ? C1D APR 1296 A 1 HETATM 32 O O2D APR . . . D 4 35.499 -33.848 19.486 1 31.01 ? O2D APR 1296 A 1 HETATM 33 C C2D APR . . . D 4 35.191 -33.089 20.693 1 35.25 ? C2D APR 1296 A 1 HETATM 34 O O3D APR . . . D 4 33.537 -32.113 19.142 1 35.9 ? O3D APR 1296 A 1 HETATM 35 C C3D APR . . . D 4 34.488 -31.845 20.162 1 32.33 ? C3D APR 1296 A 1 HETATM 36 C C4D APR . . . D 4 35.641 -30.959 19.665 1 32.18 ? C4D APR 1296 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 36 #