data_8U0I # _model_server_result.job_id vE8q6BlhFSSEE7HU5BvGWw _model_server_result.datetime_utc '2024-11-07 22:38:58' _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 8u0i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":102}' # _entry.id 8U0I # _exptl.entry_id 8U0I _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 90 _cell.angle_gamma 90 _cell.entry_id 8U0I _cell.length_a 50.317 _cell.length_b 50.317 _cell.length_c 90.596 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8U0I _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C 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 8U0I _atom_sites.fract_transf_matrix[1][1] 0.019874 _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] 0.019874 _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] 0.011038 _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 C2E A 1 101 1 C2E C2E . C 2 C2E A 1 102 2 C2E C2E . D 3 GOL A 1 103 1 GOL GOL . E 3 GOL A 1 104 2 GOL GOL . F 3 GOL A 1 105 3 GOL GOL . G 4 HOH A 1 201 73 HOH HOH . G 4 HOH A 2 202 32 HOH HOH . G 4 HOH A 3 203 83 HOH HOH . G 4 HOH A 4 204 85 HOH HOH . G 4 HOH A 5 205 4 HOH HOH . G 4 HOH A 6 206 24 HOH HOH . G 4 HOH A 7 207 48 HOH HOH . G 4 HOH A 8 208 63 HOH HOH . G 4 HOH A 9 209 41 HOH HOH . G 4 HOH A 10 210 29 HOH HOH . G 4 HOH A 11 211 33 HOH HOH . G 4 HOH A 12 212 15 HOH HOH . G 4 HOH A 13 213 71 HOH HOH . G 4 HOH A 14 214 11 HOH HOH . G 4 HOH A 15 215 89 HOH HOH . G 4 HOH A 16 216 18 HOH HOH . G 4 HOH A 17 217 19 HOH HOH . G 4 HOH A 18 218 12 HOH HOH . G 4 HOH A 19 219 49 HOH HOH . G 4 HOH A 20 220 21 HOH HOH . G 4 HOH A 21 221 5 HOH HOH . G 4 HOH A 22 222 13 HOH HOH . G 4 HOH A 23 223 64 HOH HOH . G 4 HOH A 24 224 82 HOH HOH . G 4 HOH A 25 225 54 HOH HOH . G 4 HOH A 26 226 2 HOH HOH . G 4 HOH A 27 227 9 HOH HOH . G 4 HOH A 28 228 22 HOH HOH . G 4 HOH A 29 229 14 HOH HOH . G 4 HOH A 30 230 86 HOH HOH . G 4 HOH A 31 231 20 HOH HOH . G 4 HOH A 32 232 7 HOH HOH . G 4 HOH A 33 233 69 HOH HOH . G 4 HOH A 34 234 70 HOH HOH . G 4 HOH A 35 235 62 HOH HOH . G 4 HOH A 36 236 6 HOH HOH . G 4 HOH A 37 237 44 HOH HOH . G 4 HOH A 38 238 17 HOH HOH . G 4 HOH A 39 239 25 HOH HOH . G 4 HOH A 40 240 34 HOH HOH . G 4 HOH A 41 241 42 HOH HOH . G 4 HOH A 42 242 77 HOH HOH . G 4 HOH A 43 243 39 HOH HOH . G 4 HOH A 44 244 76 HOH HOH . G 4 HOH A 45 245 27 HOH HOH . G 4 HOH A 46 246 91 HOH HOH . G 4 HOH A 47 247 1 HOH HOH . G 4 HOH A 48 248 16 HOH HOH . G 4 HOH A 49 249 3 HOH HOH . G 4 HOH A 50 250 75 HOH HOH . G 4 HOH A 51 251 26 HOH HOH . G 4 HOH A 52 252 46 HOH HOH . G 4 HOH A 53 253 84 HOH HOH . G 4 HOH A 54 254 8 HOH HOH . G 4 HOH A 55 255 35 HOH HOH . G 4 HOH A 56 256 65 HOH HOH . G 4 HOH A 57 257 30 HOH HOH . G 4 HOH A 58 258 88 HOH HOH . G 4 HOH A 59 259 55 HOH HOH . G 4 HOH A 60 260 47 HOH HOH . G 4 HOH A 61 261 38 HOH HOH . G 4 HOH A 62 262 10 HOH HOH . G 4 HOH A 63 263 37 HOH HOH . G 4 HOH A 64 264 40 HOH HOH . G 4 HOH A 65 265 36 HOH HOH . G 4 HOH A 66 266 51 HOH HOH . G 4 HOH A 67 267 90 HOH HOH . G 4 HOH A 68 268 59 HOH HOH . G 4 HOH A 69 269 56 HOH HOH . G 4 HOH A 70 270 87 HOH HOH . G 4 HOH A 71 271 23 HOH HOH . G 4 HOH A 72 272 61 HOH HOH . G 4 HOH A 73 273 74 HOH HOH . G 4 HOH A 74 274 72 HOH HOH . G 4 HOH A 75 275 57 HOH HOH . G 4 HOH A 76 276 50 HOH HOH . G 4 HOH A 77 277 66 HOH HOH . G 4 HOH A 78 278 80 HOH HOH . G 4 HOH A 79 279 52 HOH HOH . G 4 HOH A 80 280 31 HOH HOH . G 4 HOH A 81 281 58 HOH HOH . G 4 HOH A 82 282 79 HOH HOH . G 4 HOH A 83 283 68 HOH HOH . G 4 HOH A 84 284 43 HOH HOH . G 4 HOH A 85 285 60 HOH HOH . G 4 HOH A 86 286 81 HOH HOH . G 4 HOH A 87 287 28 HOH HOH . G 4 HOH A 88 288 53 HOH HOH . G 4 HOH A 89 289 45 HOH HOH . G 4 HOH A 90 290 67 HOH HOH . G 4 HOH A 91 291 78 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 . . . C 2 -8.33 4.799 -10.189 1 23.14 ? P1 C2E 102 A 1 HETATM 2 O O2P C2E . . . C 2 -8.735 5.989 -11.038 1 27.11 ? O2P C2E 102 A 1 HETATM 3 O O1P C2E . . . C 2 -7.37 3.803 -10.667 1 20.87 ? O1P C2E 102 A 1 HETATM 4 O O5' C2E . . . C 2 -9.692 4.086 -9.719 1 19.3 ? O5' C2E 102 A 1 HETATM 5 C C5' C2E . . . C 2 -10.819 4.835 -9.402 1 18.83 ? C5' C2E 102 A 1 HETATM 6 C C4' C2E . . . C 2 -11.847 3.972 -8.743 1 18.68 ? C4' C2E 102 A 1 HETATM 7 O O4' C2E . . . C 2 -12.213 2.858 -9.598 1 18.75 ? O4' C2E 102 A 1 HETATM 8 C C3' C2E . . . C 2 -11.421 3.294 -7.447 1 17.6 ? C3' C2E 102 A 1 HETATM 9 O O3' C2E . . . C 2 -11.391 4.241 -6.408 1 19.47 ? O3' C2E 102 A 1 HETATM 10 C C2' C2E . . . C 2 -12.558 2.319 -7.331 1 16.98 ? C2' C2E 102 A 1 HETATM 11 O O2' C2E . . . C 2 -13.799 2.864 -6.965 1 19.12 ? O2' C2E 102 A 1 HETATM 12 C C1' C2E . . . C 2 -12.6 1.787 -8.764 1 17.66 ? C1' C2E 102 A 1 HETATM 13 N N9 C2E . . . C 2 -11.74 0.654 -9.035 1 17.19 ? N9 C2E 102 A 1 HETATM 14 C C8 C2E . . . C 2 -10.588 0.576 -9.787 1 16.98 ? C8 C2E 102 A 1 HETATM 15 N N7 C2E . . . C 2 -10.061 -0.618 -9.858 1 19.51 ? N7 C2E 102 A 1 HETATM 16 C C5 C2E . . . C 2 -10.911 -1.365 -9.044 1 16.13 ? C5 C2E 102 A 1 HETATM 17 C C6 C2E . . . C 2 -10.83 -2.726 -8.655 1 18.62 ? C6 C2E 102 A 1 HETATM 18 O O6 C2E . . . C 2 -10.022 -3.585 -9.019 1 18.28 ? O6 C2E 102 A 1 HETATM 19 N N1 C2E . . . C 2 -11.874 -3.051 -7.79 1 17.74 ? N1 C2E 102 A 1 HETATM 20 C C2 C2E . . . C 2 -12.848 -2.213 -7.327 1 16.42 ? C2 C2E 102 A 1 HETATM 21 N N2 C2E . . . C 2 -13.725 -2.728 -6.467 1 17.93 ? N2 C2E 102 A 1 HETATM 22 N N3 C2E . . . C 2 -12.917 -0.926 -7.665 1 16.54 ? N3 C2E 102 A 1 HETATM 23 C C4 C2E . . . C 2 -11.909 -0.587 -8.504 1 17.13 ? C4 C2E 102 A 1 HETATM 24 P P11 C2E . . . C 2 -10.508 3.957 -5.088 1 19.2 ? P11 C2E 102 A 1 HETATM 25 O O21 C2E . . . C 2 -10.596 2.484 -4.792 1 18.76 ? O21 C2E 102 A 1 HETATM 26 O O11 C2E . . . C 2 -10.947 5.021 -4.134 1 18.74 ? O11 C2E 102 A 1 HETATM 27 O O5A C2E . . . C 2 -9.016 4.1 -5.6 1 19.27 ? O5A C2E 102 A 1 HETATM 28 C C5A C2E . . . C 2 -8.619 5.506 -5.866 1 22.63 ? C5A C2E 102 A 1 HETATM 29 C C4A C2E . . . C 2 -7.314 5.51 -6.588 1 22.41 ? C4A C2E 102 A 1 HETATM 30 O O4A C2E . . . C 2 -6.284 4.967 -5.733 1 21.55 ? O4A C2E 102 A 1 HETATM 31 C C3A C2E . . . C 2 -7.217 4.703 -7.869 1 21.62 ? C3A C2E 102 A 1 HETATM 32 O O3A C2E . . . C 2 -7.823 5.536 -8.875 1 23.02 ? O3A C2E 102 A 1 HETATM 33 C C2A C2E . . . C 2 -5.705 4.531 -7.983 1 21.94 ? C2A C2E 102 A 1 HETATM 34 O O2A C2E . . . C 2 -5.055 5.714 -8.45 1 24.74 ? O2A C2E 102 A 1 HETATM 35 C C1A C2E . . . C 2 -5.352 4.291 -6.532 1 19.95 ? C1A C2E 102 A 1 HETATM 36 N N91 C2E . . . C 2 -5.375 2.878 -6.166 1 21.8 ? N91 C2E 102 A 1 HETATM 37 C C81 C2E . . . C 2 -6.235 2.24 -5.311 1 21.71 ? C81 C2E 102 A 1 HETATM 38 N N71 C2E . . . C 2 -5.935 0.979 -5.169 1 20.44 ? N71 C2E 102 A 1 HETATM 39 C C51 C2E . . . C 2 -4.786 0.786 -5.912 1 21.02 ? C51 C2E 102 A 1 HETATM 40 C C61 C2E . . . C 2 -3.975 -0.36 -6.119 1 22.54 ? C61 C2E 102 A 1 HETATM 41 O O61 C2E . . . C 2 -4.121 -1.508 -5.684 1 21.5 ? O61 C2E 102 A 1 HETATM 42 N N11 C2E . . . C 2 -2.87 -0.077 -6.934 1 22.84 ? N11 C2E 102 A 1 HETATM 43 C C21 C2E . . . C 2 -2.64 1.128 -7.537 1 25.53 ? C21 C2E 102 A 1 HETATM 44 N N21 C2E . . . C 2 -1.554 1.222 -8.323 1 27.68 ? N21 C2E 102 A 1 HETATM 45 N N31 C2E . . . C 2 -3.406 2.187 -7.361 1 24.05 ? N31 C2E 102 A 1 HETATM 46 C C41 C2E . . . C 2 -4.448 1.956 -6.541 1 22.27 ? C41 C2E 102 A 1 HETATM 47 H "H5'1" C2E . . . C 2 -11.199 5.228 -10.226 1 18.95 ? "H5'1" C2E 102 A 1 HETATM 48 H "H5'2" C2E . . . C 2 -10.569 5.572 -8.793 1 18.93 ? "H5'2" C2E 102 A 1 HETATM 49 H H4' C2E . . . C 2 -12.643 4.519 -8.575 1 18.57 ? H4' C2E 102 A 1 HETATM 50 H H3' C2E . . . C 2 -10.555 2.835 -7.543 1 18.04 ? H3' C2E 102 A 1 HETATM 51 H H2' C2E . . . C 2 -12.31 1.592 -6.7 1 17.62 ? H2' C2E 102 A 1 HETATM 52 H HO2' C2E . . . C 2 -14.375 2.242 -6.926 0 19.11 ? HO2' C2E 102 A 1 HETATM 53 H H1' C2E . . . C 2 -13.526 1.538 -8.973 1 17.66 ? H1' C2E 102 A 1 HETATM 54 H H8 C2E . . . C 2 -10.271 1.298 -10.301 1 17.67 ? H8 C2E 102 A 1 HETATM 55 H HN1 C2E . . . C 2 -11.898 -3.902 -7.505 1 17.61 ? HN1 C2E 102 A 1 HETATM 56 H HN21 C2E . . . C 2 -14.359 -2.222 -6.135 1 17.46 ? HN21 C2E 102 A 1 HETATM 57 H HN22 C2E . . . C 2 -13.669 -3.572 -6.235 1 17.46 ? HN22 C2E 102 A 1 HETATM 58 H H511 C2E . . . C 2 -8.53 5.998 -5.013 1 21.76 ? H511 C2E 102 A 1 HETATM 59 H H512 C2E . . . C 2 -9.307 5.953 -6.419 1 21.73 ? H512 C2E 102 A 1 HETATM 60 H H4A C2E . . . C 2 -7.089 6.443 -6.788 1 22.14 ? H4A C2E 102 A 1 HETATM 61 H H3A C2E . . . C 2 -7.679 3.838 -7.791 1 22.05 ? H3A C2E 102 A 1 HETATM 62 H H2A C2E . . . C 2 -5.473 3.747 -8.545 1 22.01 ? H2A C2E 102 A 1 HETATM 63 H HO2A C2E . . . C 2 -4.219 5.571 -8.497 0 24.76 ? HO2A C2E 102 A 1 HETATM 64 H H1A C2E . . . C 2 -4.453 4.653 -6.363 1 20.98 ? H1A C2E 102 A 1 HETATM 65 H H81 C2E . . . C 2 -6.99 2.646 -4.924 1 21.41 ? H81 C2E 102 A 1 HETATM 66 H HN11 C2E . . . C 2 -2.343 -0.767 -7.155 1 23.44 ? HN11 C2E 102 A 1 HETATM 67 H HN24 C2E . . . C 2 -1.372 1.978 -8.728 1 26.85 ? HN24 C2E 102 A 1 HETATM 68 H HN23 C2E . . . C 2 -1.028 0.527 -8.43 1 26.9 ? HN23 C2E 102 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 68 #