data_4CWB # _model_server_result.job_id XpeR2ApoN6rcBhZCdsol6g _model_server_result.datetime_utc '2024-11-23 10:52:10' _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 4cwb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1161}' # _entry.id 4CWB # _exptl.entry_id 4CWB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 4CWB _cell.length_a 83.817 _cell.length_b 83.817 _cell.length_c 52.04 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CWB _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 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 A OD2 ASP 98 A ASP 95 1_555 B MG MG . A MG 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc2 A OD1 ASP 98 A ASP 95 1_555 C MG MG . A MG 1160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc3 A OD2 ASP 100 A ASP 97 1_555 B MG MG . A MG 1159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc4 A OD1 ASP 100 A ASP 97 1_555 C MG MG . A MG 1160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc5 B MG MG . A MG 1159 1_555 D O1B APC . A APC 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc6 B MG MG . A MG 1159 1_555 D O3G APC . A APC 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc7 B MG MG . A MG 1159 1_555 G O HOH . A HOH 2083 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc8 B MG MG . A MG 1159 1_555 G O HOH . A HOH 2084 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc9 C MG MG . A MG 1160 1_555 D O1B APC . A APC 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc10 C MG MG . A MG 1160 1_555 D O1A APC . A APC 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc11 C MG MG . A MG 1160 1_555 G O HOH . A HOH 2065 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc12 C MG MG . A MG 1160 1_555 G O HOH . A HOH 2085 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 PG O1G APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 4CWB _atom_sites.fract_transf_matrix[1][1] 0.011931 _atom_sites.fract_transf_matrix[1][2] 0.006888 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013776 _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] 0.019216 _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 MG A 1 1159 1159 MG MG . C 2 MG A 1 1160 1160 MG MG . D 3 APC A 1 1161 1161 APC APC . E 4 NO3 A 1 1162 1162 NO3 NO3 . F 5 X6L A 1 1163 1163 X6L X6L . 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 . # 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 P PG APC . . . D 3 39.492 -14.263 -19.433 1 11.67 ? PG APC 1161 A 1 HETATM 2 O O1G APC . . . D 3 40.701 -15.201 -19.602 1 12.75 ? O1G APC 1161 A 1 HETATM 3 O O2G APC . . . D 3 38.246 -14.957 -18.903 1 12.58 ? O2G APC 1161 A 1 HETATM 4 O O3G APC . . . D 3 39.882 -13.025 -18.723 1 9.97 ? O3G APC 1161 A 1 HETATM 5 P PB APC . . . D 3 37.905 -12.882 -21.307 1 11.93 ? PB APC 1161 A 1 HETATM 6 O O1B APC . . . D 3 37.444 -12.181 -20.038 1 12.6 ? O1B APC 1161 A 1 HETATM 7 O O2B APC . . . D 3 38.395 -11.879 -22.447 1 13.81 ? O2B APC 1161 A 1 HETATM 8 O O3B APC . . . D 3 39.146 -13.821 -20.941 1 11.92 ? O3B APC 1161 A 1 HETATM 9 P PA APC . . . D 3 35.032 -13.353 -22.133 1 12.74 ? PA APC 1161 A 1 HETATM 10 O O1A APC . . . D 3 34.755 -12.262 -21.137 1 10.78 ? O1A APC 1161 A 1 HETATM 11 O O2A APC . . . D 3 35.018 -12.854 -23.651 1 13.94 ? O2A APC 1161 A 1 HETATM 12 C C3A APC . . . D 3 36.647 -14.054 -21.851 1 12.26 ? C3A APC 1161 A 1 HETATM 13 O O5' APC . . . D 3 33.916 -14.446 -21.721 1 15.94 ? O5' APC 1161 A 1 HETATM 14 C C5' APC . . . D 3 33.698 -15.644 -22.422 1 18.93 ? C5' APC 1161 A 1 HETATM 15 C C4' APC . . . D 3 33.253 -16.717 -21.442 1 18.07 ? C4' APC 1161 A 1 HETATM 16 O O4' APC . . . D 3 34.288 -17.007 -20.492 1 16.93 ? O4' APC 1161 A 1 HETATM 17 C C3' APC . . . D 3 32.041 -16.464 -20.565 1 18.23 ? C3' APC 1161 A 1 HETATM 18 O O3' APC . . . D 3 30.77 -16.442 -21.236 1 19.41 ? O3' APC 1161 A 1 HETATM 19 C C2' APC . . . D 3 32.182 -17.651 -19.619 1 17.03 ? C2' APC 1161 A 1 HETATM 20 O O2' APC . . . D 3 31.464 -18.797 -20.124 1 18.94 ? O2' APC 1161 A 1 HETATM 21 C C1' APC . . . D 3 33.669 -17.954 -19.644 1 16.65 ? C1' APC 1161 A 1 HETATM 22 N N9 APC . . . D 3 34.232 -17.986 -18.28 1 14.17 ? N9 APC 1161 A 1 HETATM 23 C C8 APC . . . D 3 34.822 -19.082 -17.752 1 14.43 ? C8 APC 1161 A 1 HETATM 24 N N7 APC . . . D 3 35.202 -18.868 -16.477 1 12.65 ? N7 APC 1161 A 1 HETATM 25 C C5 APC . . . D 3 34.807 -17.591 -16.179 1 12.25 ? C5 APC 1161 A 1 HETATM 26 C C6 APC . . . D 3 34.92 -16.732 -14.994 1 11.32 ? C6 APC 1161 A 1 HETATM 27 N N6 APC . . . D 3 35.51 -17.175 -13.86 1 10.96 ? N6 APC 1161 A 1 HETATM 28 N N1 APC . . . D 3 34.401 -15.495 -15.117 1 10.32 ? N1 APC 1161 A 1 HETATM 29 C C2 APC . . . D 3 33.81 -15.027 -16.229 1 12.19 ? C2 APC 1161 A 1 HETATM 30 N N3 APC . . . D 3 33.7 -15.755 -17.351 1 12.85 ? N3 APC 1161 A 1 HETATM 31 C C4 APC . . . D 3 34.169 -17.019 -17.36 1 13.61 ? C4 APC 1161 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #