data_8WJD # _model_server_result.job_id HUEqri6fVNI-zudwEaoXaw _model_server_result.datetime_utc '2024-11-28 11:12:01' _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 8wjd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8WJD # _exptl.entry_id 8WJD _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 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 8WJD _cell.length_a 61.55 _cell.length_b 61.55 _cell.length_c 97.51 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WJD _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -61.55 0 0 3 'crystal symmetry operation' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 11_455 -x+y-1,y,-z -1 0 0 0 1 0 0 0 -1 -61.55 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 8WJD _atom_sites.fract_transf_matrix[1][1] 0.016247 _atom_sites.fract_transf_matrix[1][2] 0.00938 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01876 _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] 0.010255 _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 1 201 181 C2E C2E . C 3 HOH A 1 301 24 HOH HOH . C 3 HOH A 2 302 15 HOH HOH . C 3 HOH A 3 303 6 HOH HOH . C 3 HOH A 4 304 26 HOH HOH . C 3 HOH A 5 305 1 HOH HOH . C 3 HOH A 6 306 45 HOH HOH . C 3 HOH A 7 307 10 HOH HOH . C 3 HOH A 8 308 5 HOH HOH . C 3 HOH A 9 309 42 HOH HOH . C 3 HOH A 10 310 37 HOH HOH . C 3 HOH A 11 311 3 HOH HOH . C 3 HOH A 12 312 19 HOH HOH . C 3 HOH A 13 313 2 HOH HOH . C 3 HOH A 14 314 25 HOH HOH . C 3 HOH A 15 315 8 HOH HOH . C 3 HOH A 16 316 9 HOH HOH . C 3 HOH A 17 317 39 HOH HOH . C 3 HOH A 18 318 21 HOH HOH . C 3 HOH A 19 319 12 HOH HOH . C 3 HOH A 20 320 22 HOH HOH . C 3 HOH A 21 321 7 HOH HOH . C 3 HOH A 22 322 4 HOH HOH . C 3 HOH A 23 323 28 HOH HOH . C 3 HOH A 24 324 29 HOH HOH . C 3 HOH A 25 325 14 HOH HOH . C 3 HOH A 26 326 44 HOH HOH . C 3 HOH A 27 327 17 HOH HOH . C 3 HOH A 28 328 40 HOH HOH . C 3 HOH A 29 329 27 HOH HOH . C 3 HOH A 30 330 16 HOH HOH . C 3 HOH A 31 331 18 HOH HOH . C 3 HOH A 32 332 33 HOH HOH . C 3 HOH A 33 333 13 HOH HOH . C 3 HOH A 34 334 38 HOH HOH . C 3 HOH A 35 335 20 HOH HOH . C 3 HOH A 36 336 30 HOH HOH . C 3 HOH A 37 337 32 HOH HOH . C 3 HOH A 38 338 43 HOH HOH . C 3 HOH A 39 339 34 HOH HOH . C 3 HOH A 40 340 11 HOH HOH . C 3 HOH A 41 341 36 HOH HOH . C 3 HOH A 42 342 31 HOH HOH . C 3 HOH A 43 343 41 HOH HOH . C 3 HOH A 44 344 23 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 . . . B 2 -31.995 -2.573 -25.379 0.42 28.69 ? P1 C2E 201 A 1 HETATM 2 O O2P C2E . . . B 2 -31.845 -3.193 -24.033 0.42 29.65 ? O2P C2E 201 A 1 HETATM 3 O O1P C2E . . . B 2 -32.693 -3.355 -26.44 0.42 30.44 ? O1P C2E 201 A 1 HETATM 4 O O5' C2E . . . B 2 -32.691 -1.143 -25.228 0.42 26.34 ? O5' C2E 201 A 1 HETATM 5 C C5' C2E . . . B 2 -32.936 -0.38 -26.425 0.42 28.17 ? C5' C2E 201 A 1 HETATM 6 C C4' C2E . . . B 2 -33.222 1.038 -26.008 0.42 24.98 ? C4' C2E 201 A 1 HETATM 7 O O4' C2E . . . B 2 -34.403 1.069 -25.183 0.42 26.08 ? O4' C2E 201 A 1 HETATM 8 C C3' C2E . . . B 2 -32.135 1.662 -25.142 0.42 25.05 ? C3' C2E 201 A 1 HETATM 9 O O3' C2E . . . B 2 -31.068 2.119 -25.962 0.42 26.25 ? O3' C2E 201 A 1 HETATM 10 C C2' C2E . . . B 2 -32.912 2.806 -24.491 0.42 30.47 ? C2' C2E 201 A 1 HETATM 11 O O2' C2E . . . B 2 -33.07 3.879 -25.394 0.42 30.52 ? O2' C2E 201 A 1 HETATM 12 C C1' C2E . . . B 2 -34.259 2.125 -24.238 0.42 27.07 ? C1' C2E 201 A 1 HETATM 13 N N9 C2E . . . B 2 -34.344 1.555 -22.897 0.42 27.39 ? N9 C2E 201 A 1 HETATM 14 C C8 C2E . . . B 2 -34.438 0.243 -22.509 0.42 28.21 ? C8 C2E 201 A 1 HETATM 15 N N7 C2E . . . B 2 -34.496 0.088 -21.206 0.42 23.98 ? N7 C2E 201 A 1 HETATM 16 C C5 C2E . . . B 2 -34.443 1.388 -20.711 0.42 25.27 ? C5 C2E 201 A 1 HETATM 17 C C6 C2E . . . B 2 -34.466 1.854 -19.374 0.42 28.89 ? C6 C2E 201 A 1 HETATM 18 O O6 C2E . . . B 2 -34.543 1.184 -18.334 0.42 25.37 ? O6 C2E 201 A 1 HETATM 19 N N1 C2E . . . B 2 -34.393 3.248 -19.317 0.42 24.76 ? N1 C2E 201 A 1 HETATM 20 C C2 C2E . . . B 2 -34.288 4.085 -20.406 0.42 31.89 ? C2 C2E 201 A 1 HETATM 21 N N2 C2E . . . B 2 -34.214 5.403 -20.157 0.42 30.63 ? N2 C2E 201 A 1 HETATM 22 N N3 C2E . . . B 2 -34.274 3.652 -21.664 0.42 26.42 ? N3 C2E 201 A 1 HETATM 23 C C4 C2E . . . B 2 -34.348 2.302 -21.737 0.42 26.41 ? C4 C2E 201 A 1 HETATM 24 P P11 C2E . . . B 2 -29.643 2.521 -25.335 0.42 28.58 ? P11 C2E 201 A 1 HETATM 25 O O21 C2E . . . B 2 -29.817 3.107 -23.978 0.42 29.71 ? O21 C2E 201 A 1 HETATM 26 O O11 C2E . . . B 2 -28.906 3.32 -26.357 0.42 30.38 ? O11 C2E 201 A 1 HETATM 27 O O5A C2E . . . B 2 -28.959 1.084 -25.199 0.42 26.35 ? O5A C2E 201 A 1 HETATM 28 C C5A C2E . . . B 2 -28.696 0.336 -26.403 0.42 28.15 ? C5A C2E 201 A 1 HETATM 29 C C4A C2E . . . B 2 -28.412 -1.086 -25.997 0.42 25.06 ? C4A C2E 201 A 1 HETATM 30 O O4A C2E . . . B 2 -27.232 -1.123 -25.171 0.42 26.06 ? O4A C2E 201 A 1 HETATM 31 C C3A C2E . . . B 2 -29.505 -1.705 -25.135 0.42 25.06 ? C3A C2E 201 A 1 HETATM 32 O O3A C2E . . . B 2 -30.56 -2.157 -25.974 0.42 26.3 ? O3A C2E 201 A 1 HETATM 33 C C2A C2E . . . B 2 -28.737 -2.842 -24.458 0.42 30.5 ? C2A C2E 201 A 1 HETATM 34 O O2A C2E . . . B 2 -28.578 -3.941 -25.33 0.42 30.48 ? O2A C2E 201 A 1 HETATM 35 C C1A C2E . . . B 2 -27.383 -2.17 -24.218 0.42 27.09 ? C1A C2E 201 A 1 HETATM 36 N N91 C2E . . . B 2 -27.279 -1.59 -22.883 0.42 27.34 ? N91 C2E 201 A 1 HETATM 37 C C81 C2E . . . B 2 -27.194 -0.275 -22.505 0.42 28.22 ? C81 C2E 201 A 1 HETATM 38 N N71 C2E . . . B 2 -27.11 -0.11 -21.205 0.42 23.99 ? N71 C2E 201 A 1 HETATM 39 C C51 C2E . . . B 2 -27.137 -1.408 -20.701 0.42 25.27 ? C51 C2E 201 A 1 HETATM 40 C C61 C2E . . . B 2 -27.082 -1.866 -19.362 0.42 28.89 ? C61 C2E 201 A 1 HETATM 41 O O61 C2E . . . B 2 -26.991 -1.188 -18.328 0.42 25.38 ? O61 C2E 201 A 1 HETATM 42 N N11 C2E . . . B 2 -27.136 -3.26 -19.296 0.42 24.71 ? N11 C2E 201 A 1 HETATM 43 C C21 C2E . . . B 2 -27.253 -4.105 -20.378 0.42 31.9 ? C21 C2E 201 A 1 HETATM 44 N N21 C2E . . . B 2 -27.305 -5.422 -20.119 0.42 30.66 ? N21 C2E 201 A 1 HETATM 45 N N31 C2E . . . B 2 -27.297 -3.68 -21.638 0.42 26.44 ? N31 C2E 201 A 1 HETATM 46 C C41 C2E . . . B 2 -27.241 -2.329 -21.719 0.42 26.42 ? C41 C2E 201 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #