data_4URG # _model_server_result.job_id 1fgPgXq2s6ykt_xORKPHCA _model_server_result.datetime_utc '2025-07-16 01:38:13' _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 4urg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1241}' # _entry.id 4URG # _exptl.entry_id 4URG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 124.05 _cell.angle_gamma 90 _cell.entry_id 4URG _cell.length_a 108.89 _cell.length_b 52.12 _cell.length_c 73.71 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4URG _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E 1 1 B,F 2 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 ? 2 C N N ? 2 D N N # _chem_comp.formula 'C20 H24 N10 O14 P2' _chem_comp.formula_weight 690.411 _chem_comp.id C2E _chem_comp.mon_nstd_flag . _chem_comp.name "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'c-di-GMP;Cyclic diguanosine monophosphate' # 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 P1 O2P C2E sing 70 n n O1P P1 C2E doub 71 n n O5' P1 C2E sing 72 n n C5' O5' C2E sing 73 n n C4' O4' C2E sing 74 n n C4' C5' C2E sing 75 n n C3' C4' C2E sing 76 n n O3' P11 C2E sing 77 n n O3' C3' C2E sing 78 n n C2' C3' C2E sing 79 n n C2' C1' C2E sing 80 n n O2' C2' C2E sing 81 n n C1' O4' C2E sing 82 n n C1' N9 C2E sing 83 n n N9 C4 C2E sing 84 n y N9 C8 C2E sing 85 n y C8 N7 C2E doub 86 n y C5 N7 C2E sing 87 n y C5 C6 C2E sing 88 n n C6 O6 C2E doub 89 n n N1 C6 C2E sing 90 n n C2 N1 C2E sing 91 n n N2 C2 C2E sing 92 n n N3 C2 C2E doub 93 n n N3 C4 C2E sing 94 n n C4 C5 C2E doub 95 n y P11 O21 C2E sing 96 n n P11 O5A C2E sing 97 n n O11 P11 C2E doub 98 n n C5A O5A C2E sing 99 n n C5A C4A C2E sing 100 n n C4A O4A C2E sing 101 n n C4A C3A C2E sing 102 n n O4A C1A C2E sing 103 n n C3A C2A C2E sing 104 n n O3A C3A C2E sing 105 n n O3A P1 C2E sing 106 n n C2A O2A C2E sing 107 n n C1A C2A C2E sing 108 n n C1A N91 C2E sing 109 n n N91 C41 C2E sing 110 n y C81 N71 C2E doub 111 n y C81 N91 C2E sing 112 n y N71 C51 C2E sing 113 n y C51 C41 C2E doub 114 n y C51 C61 C2E sing 115 n n C61 O61 C2E doub 116 n n C61 N11 C2E sing 117 n n C21 N11 C2E sing 118 n n C21 N21 C2E sing 119 n n N31 C21 C2E doub 120 n n C41 N31 C2E sing 121 n n O2P HO2P C2E sing 122 n n C5' "H5'1" C2E sing 123 n n C5' "H5'2" C2E sing 124 n n C4' H4' C2E sing 125 n n C3' H3' C2E sing 126 n n C2' H2' C2E sing 127 n n O2' HO2' C2E sing 128 n n C1' H1' C2E sing 129 n n C8 H8 C2E sing 130 n n N1 HN1 C2E sing 131 n n N2 HN21 C2E sing 132 n n N2 HN22 C2E sing 133 n n O21 HO21 C2E sing 134 n n C5A H511 C2E sing 135 n n C5A H512 C2E sing 136 n n C4A H4A C2E sing 137 n n C3A H3A C2E sing 138 n n C2A H2A C2E sing 139 n n O2A HO2A C2E sing 140 n n C1A H1A C2E sing 141 n n C81 H81 C2E sing 142 n n N11 HN11 C2E sing 143 n n N21 HN24 C2E sing 144 n n N21 HN23 C2E sing 145 n n # _atom_sites.entry_id 4URG _atom_sites.fract_transf_matrix[1][1] 0.009184 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006206 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019186 _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] 0.016374 _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 2 C2E A 1 1240 1240 C2E C2E . D 2 C2E A 1 1241 1241 C2E C2E . E 3 HOH A 1 2001 2001 HOH HOH . E 3 HOH A 2 2002 2002 HOH HOH . E 3 HOH A 3 2003 2003 HOH HOH . E 3 HOH A 4 2004 2004 HOH HOH . E 3 HOH A 5 2005 2005 HOH HOH . E 3 HOH A 6 2006 2006 HOH HOH . E 3 HOH A 7 2007 2007 HOH HOH . E 3 HOH A 8 2008 2008 HOH HOH . E 3 HOH A 9 2009 2009 HOH HOH . E 3 HOH A 10 2010 2010 HOH HOH . E 3 HOH A 11 2011 2011 HOH HOH . E 3 HOH A 12 2012 2012 HOH HOH . E 3 HOH A 13 2013 2013 HOH HOH . E 3 HOH A 14 2014 2014 HOH HOH . E 3 HOH A 15 2015 2015 HOH HOH . E 3 HOH A 16 2016 2016 HOH HOH . E 3 HOH A 17 2017 2017 HOH HOH . E 3 HOH A 18 2018 2018 HOH HOH . E 3 HOH A 19 2019 2019 HOH HOH . E 3 HOH A 20 2020 2020 HOH HOH . E 3 HOH A 21 2021 2021 HOH HOH . E 3 HOH A 22 2022 2022 HOH HOH . E 3 HOH A 23 2023 2023 HOH HOH . E 3 HOH A 24 2024 2024 HOH HOH . E 3 HOH A 25 2025 2025 HOH HOH . E 3 HOH A 26 2026 2026 HOH HOH . E 3 HOH A 27 2027 2027 HOH HOH . E 3 HOH A 28 2028 2028 HOH HOH . E 3 HOH A 29 2029 2029 HOH HOH . E 3 HOH A 30 2030 2030 HOH HOH . E 3 HOH A 31 2031 2031 HOH HOH . E 3 HOH A 32 2032 2032 HOH HOH . E 3 HOH A 33 2033 2033 HOH HOH . E 3 HOH A 34 2034 2034 HOH HOH . E 3 HOH A 35 2035 2035 HOH HOH . E 3 HOH A 36 2036 2036 HOH HOH . E 3 HOH A 37 2037 2037 HOH HOH . E 3 HOH A 38 2038 2038 HOH HOH . E 3 HOH A 39 2039 2039 HOH HOH . E 3 HOH A 40 2040 2040 HOH HOH . E 3 HOH A 41 2041 2041 HOH HOH . E 3 HOH A 42 2042 2042 HOH HOH . E 3 HOH A 43 2043 2043 HOH HOH . E 3 HOH A 44 2044 2044 HOH HOH . E 3 HOH A 45 2045 2045 HOH HOH . E 3 HOH A 46 2046 2046 HOH HOH . E 3 HOH A 47 2047 2047 HOH HOH . E 3 HOH A 48 2048 2048 HOH HOH . E 3 HOH A 49 2049 2049 HOH HOH . E 3 HOH A 50 2050 2050 HOH HOH . E 3 HOH A 51 2051 2051 HOH HOH . E 3 HOH A 52 2052 2052 HOH HOH . E 3 HOH A 53 2053 2053 HOH HOH . E 3 HOH A 54 2054 2054 HOH HOH . E 3 HOH A 55 2055 2055 HOH HOH . E 3 HOH A 56 2056 2056 HOH HOH . E 3 HOH A 57 2057 2057 HOH HOH . E 3 HOH A 58 2058 2058 HOH HOH . E 3 HOH A 59 2059 2059 HOH HOH . E 3 HOH A 60 2060 2060 HOH HOH . E 3 HOH A 61 2061 2061 HOH HOH . E 3 HOH A 62 2062 2062 HOH HOH . E 3 HOH A 63 2063 2063 HOH HOH . E 3 HOH A 64 2064 2064 HOH HOH . E 3 HOH A 65 2065 2065 HOH HOH . E 3 HOH A 66 2066 2066 HOH HOH . E 3 HOH A 67 2067 2067 HOH HOH . E 3 HOH A 68 2068 2068 HOH HOH . E 3 HOH A 69 2069 2069 HOH HOH . E 3 HOH A 70 2070 2070 HOH HOH . E 3 HOH A 71 2071 2071 HOH HOH . E 3 HOH A 72 2072 2072 HOH HOH . E 3 HOH A 73 2073 2073 HOH HOH . E 3 HOH A 74 2074 2074 HOH HOH . E 3 HOH A 75 2075 2075 HOH HOH . E 3 HOH A 76 2076 2076 HOH HOH . E 3 HOH A 77 2077 2077 HOH HOH . E 3 HOH A 78 2078 2078 HOH HOH . E 3 HOH A 79 2079 2079 HOH HOH . E 3 HOH A 80 2080 2080 HOH HOH . E 3 HOH A 81 2081 2081 HOH HOH . E 3 HOH A 82 2082 2082 HOH HOH . E 3 HOH A 83 2083 2083 HOH HOH . E 3 HOH A 84 2084 2084 HOH HOH . E 3 HOH A 85 2085 2085 HOH HOH . E 3 HOH A 86 2086 2086 HOH HOH . E 3 HOH A 87 2087 2087 HOH HOH . E 3 HOH A 88 2088 2088 HOH HOH . E 3 HOH A 89 2089 2089 HOH HOH . E 3 HOH A 90 2090 2090 HOH HOH . E 3 HOH A 91 2091 2091 HOH HOH . E 3 HOH A 92 2092 2092 HOH HOH . F 3 HOH B 1 2001 2001 HOH HOH . F 3 HOH B 2 2002 2002 HOH HOH . F 3 HOH B 3 2003 2003 HOH HOH . F 3 HOH B 4 2004 2004 HOH HOH . F 3 HOH B 5 2005 2005 HOH HOH . F 3 HOH B 6 2006 2006 HOH HOH . F 3 HOH B 7 2007 2007 HOH HOH . F 3 HOH B 8 2008 2008 HOH HOH . F 3 HOH B 9 2009 2009 HOH HOH . F 3 HOH B 10 2010 2010 HOH HOH . F 3 HOH B 11 2011 2011 HOH HOH . F 3 HOH B 12 2012 2012 HOH HOH . F 3 HOH B 13 2013 2013 HOH HOH . F 3 HOH B 14 2014 2014 HOH HOH . F 3 HOH B 15 2015 2015 HOH HOH . F 3 HOH B 16 2016 2016 HOH HOH . F 3 HOH B 17 2017 2017 HOH HOH . F 3 HOH B 18 2018 2018 HOH HOH . F 3 HOH B 19 2019 2019 HOH HOH . F 3 HOH B 20 2020 2020 HOH HOH . F 3 HOH B 21 2021 2021 HOH HOH . F 3 HOH B 22 2022 2022 HOH HOH . F 3 HOH B 23 2023 2023 HOH HOH . F 3 HOH B 24 2024 2024 HOH HOH . F 3 HOH B 25 2025 2025 HOH HOH . F 3 HOH B 26 2026 2026 HOH HOH . F 3 HOH B 27 2027 2027 HOH HOH . F 3 HOH B 28 2028 2028 HOH HOH . F 3 HOH B 29 2029 2029 HOH HOH . F 3 HOH B 30 2030 2030 HOH HOH . F 3 HOH B 31 2031 2031 HOH HOH . F 3 HOH B 32 2032 2032 HOH HOH . F 3 HOH B 33 2033 2033 HOH HOH . F 3 HOH B 34 2034 2034 HOH HOH . F 3 HOH B 35 2035 2035 HOH HOH . F 3 HOH B 36 2036 2036 HOH HOH . F 3 HOH B 37 2037 2037 HOH HOH . F 3 HOH B 38 2038 2038 HOH HOH . F 3 HOH B 39 2039 2039 HOH HOH . F 3 HOH B 40 2040 2040 HOH HOH . F 3 HOH B 41 2041 2041 HOH HOH . F 3 HOH B 42 2042 2042 HOH HOH . F 3 HOH B 43 2043 2043 HOH HOH . F 3 HOH B 44 2044 2044 HOH HOH . F 3 HOH B 45 2045 2045 HOH HOH . F 3 HOH B 46 2046 2046 HOH HOH . F 3 HOH B 47 2047 2047 HOH HOH . F 3 HOH B 48 2048 2048 HOH HOH . F 3 HOH B 49 2049 2049 HOH HOH . F 3 HOH B 50 2050 2050 HOH HOH . F 3 HOH B 51 2051 2051 HOH HOH . F 3 HOH B 52 2052 2052 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 P1 C2E . . . D 2 21.844 15.398 9.681 1 11.5 ? P1 C2E 1241 A 1 HETATM 2 O O2P C2E . . . D 2 20.999 16.593 9.925 1 10.5 ? O2P C2E 1241 A 1 HETATM 3 O O1P C2E . . . D 2 23.236 15.42 10.155 1 7.71 ? O1P C2E 1241 A 1 HETATM 4 O O5' C2E . . . D 2 21.87 15.163 8.101 1 10.42 ? O5' C2E 1241 A 1 HETATM 5 C C5' C2E . . . D 2 20.658 15.262 7.308 1 8.87 ? C5' C2E 1241 A 1 HETATM 6 C C4' C2E . . . D 2 20.923 14.7 5.943 1 11.05 ? C4' C2E 1241 A 1 HETATM 7 O O4' C2E . . . D 2 21.984 15.452 5.312 1 9.42 ? O4' C2E 1241 A 1 HETATM 8 C C3' C2E . . . D 2 21.456 13.274 6.045 1 11.25 ? C3' C2E 1241 A 1 HETATM 9 O O3' C2E . . . D 2 20.357 12.352 6.142 1 12.03 ? O3' C2E 1241 A 1 HETATM 10 C C2' C2E . . . D 2 22.204 13.136 4.736 1 9.12 ? C2' C2E 1241 A 1 HETATM 11 O O2' C2E . . . D 2 21.245 12.945 3.612 1 10.4 ? O2' C2E 1241 A 1 HETATM 12 C C1' C2E . . . D 2 22.849 14.548 4.642 1 7.88 ? C1' C2E 1241 A 1 HETATM 13 N N9 C2E . . . D 2 24.204 14.601 5.218 1 9.58 ? N9 C2E 1241 A 1 HETATM 14 C C8 C2E . . . D 2 24.619 15.284 6.3 1 9.4 ? C8 C2E 1241 A 1 HETATM 15 N N7 C2E . . . D 2 25.925 15.082 6.422 1 9.44 ? N7 C2E 1241 A 1 HETATM 16 C C5 C2E . . . D 2 26.306 14.254 5.447 1 8.63 ? C5 C2E 1241 A 1 HETATM 17 C C6 C2E . . . D 2 27.492 13.777 5.062 1 12.81 ? C6 C2E 1241 A 1 HETATM 18 O O6 C2E . . . D 2 28.566 14.136 5.779 1 12.56 ? O6 C2E 1241 A 1 HETATM 19 N N1 C2E . . . D 2 27.623 12.969 4.005 1 14.29 ? N1 C2E 1241 A 1 HETATM 20 C C2 C2E . . . D 2 26.563 12.694 3.226 1 14.15 ? C2 C2E 1241 A 1 HETATM 21 N N2 C2E . . . D 2 26.706 11.889 2.169 1 16.16 ? N2 C2E 1241 A 1 HETATM 22 N N3 C2E . . . D 2 25.369 13.205 3.566 1 11.84 ? N3 C2E 1241 A 1 HETATM 23 C C4 C2E . . . D 2 25.255 14.009 4.66 1 9.41 ? C4 C2E 1241 A 1 HETATM 24 P P11 C2E . . . D 2 20.607 10.811 6.613 1 9.53 ? P11 C2E 1241 A 1 HETATM 25 O O21 C2E . . . D 2 21.743 10.211 5.899 1 8.79 ? O21 C2E 1241 A 1 HETATM 26 O O11 C2E . . . D 2 19.261 10.15 6.445 1 10.45 ? O11 C2E 1241 A 1 HETATM 27 O O5A C2E . . . D 2 20.964 10.886 8.113 1 8.99 ? O5A C2E 1241 A 1 HETATM 28 C C5A C2E . . . D 2 19.945 11.387 9.062 1 10.75 ? C5A C2E 1241 A 1 HETATM 29 C C4A C2E . . . D 2 20.576 11.746 10.411 1 11.02 ? C4A C2E 1241 A 1 HETATM 30 O O4A C2E . . . D 2 21.283 10.61 10.937 1 9.33 ? O4A C2E 1241 A 1 HETATM 31 C C3A C2E . . . D 2 21.627 12.836 10.289 1 10.89 ? C3A C2E 1241 A 1 HETATM 32 O O3A C2E . . . D 2 21.031 14.138 10.244 1 14.02 ? O3A C2E 1241 A 1 HETATM 33 C C2A C2E . . . D 2 22.416 12.622 11.587 1 6.87 ? C2A C2E 1241 A 1 HETATM 34 O O2A C2E . . . D 2 21.716 13.108 12.752 1 11.12 ? O2A C2E 1241 A 1 HETATM 35 C C1A C2E . . . D 2 22.428 11.078 11.664 1 6.36 ? C1A C2E 1241 A 1 HETATM 36 N N91 C2E . . . D 2 23.63 10.521 10.993 1 4.97 ? N91 C2E 1241 A 1 HETATM 37 C C81 C2E . . . D 2 23.685 9.882 9.81 1 9.73 ? C81 C2E 1241 A 1 HETATM 38 N N71 C2E . . . D 2 24.943 9.478 9.601 1 7.26 ? N71 C2E 1241 A 1 HETATM 39 C C51 C2E . . . D 2 25.664 9.9 10.639 1 6.46 ? C51 C2E 1241 A 1 HETATM 40 C C61 C2E . . . D 2 26.982 9.921 10.892 1 10.48 ? C61 C2E 1241 A 1 HETATM 41 O O61 C2E . . . D 2 27.809 9.25 10.064 1 11.51 ? O61 C2E 1241 A 1 HETATM 42 N N11 C2E . . . D 2 27.465 10.456 12.013 1 10.81 ? N11 C2E 1241 A 1 HETATM 43 C C21 C2E . . . D 2 26.67 11.107 12.85 1 10.6 ? C21 C2E 1241 A 1 HETATM 44 N N21 C2E . . . D 2 27.185 11.63 13.945 1 10.12 ? N21 C2E 1241 A 1 HETATM 45 N N31 C2E . . . D 2 25.35 11.159 12.59 1 9.34 ? N31 C2E 1241 A 1 HETATM 46 C C41 C2E . . . D 2 24.864 10.6 11.463 1 6.21 ? C41 C2E 1241 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #