data_7U3A # _model_server_result.job_id Zmr3vzmA611p9xYGYsPugg _model_server_result.datetime_utc '2024-11-05 01:26:00' _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 7u3a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 7U3A # _exptl.entry_id 7U3A _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.73 _cell.angle_gamma 90 _cell.entry_id 7U3A _cell.length_a 129.47 _cell.length_b 127.66 _cell.length_c 179.72 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7U3A _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E,F 1 1 C,D,G,H 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 E N N ? 2 F N N ? 2 G N N ? 2 H 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 7U3A _atom_sites.fract_transf_matrix[1][1] 0.007724 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000504 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007833 _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] 0.005576 _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 E 2 C2E A 1 801 201 C2E C2E . F 2 C2E B 1 801 201 C2E C2E . G 2 C2E C 1 801 201 C2E C2E . H 2 C2E D 1 801 201 C2E C2E . # 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 . . . E 2 83.552 -6.115 33.934 1 49.42 ? P1 C2E 801 A 1 HETATM 2 O O2P C2E . . . E 2 83.149 -6.057 35.393 1 42.47 ? O2P C2E 801 A 1 HETATM 3 O O1P C2E . . . E 2 82.259 -5.926 33.179 1 48.51 ? O1P C2E 801 A 1 HETATM 4 O O5' C2E . . . E 2 84.104 -7.638 33.425 1 43.52 ? O5' C2E 801 A 1 HETATM 5 C C5' C2E . . . E 2 85.431 -8.079 33.799 1 42.73 ? C5' C2E 801 A 1 HETATM 6 C C4' C2E . . . E 2 85.911 -9.25 32.781 1 47.95 ? C4' C2E 801 A 1 HETATM 7 O O4' C2E . . . E 2 84.895 -10.451 32.794 1 49.33 ? O4' C2E 801 A 1 HETATM 8 C C3' C2E . . . E 2 85.924 -8.818 31.629 1 47.75 ? C3' C2E 801 A 1 HETATM 9 O O3' C2E . . . E 2 87.349 -8.494 31.231 1 47.47 ? O3' C2E 801 A 1 HETATM 10 C C2' C2E . . . E 2 85.311 -10.027 30.655 1 44 ? C2' C2E 801 A 1 HETATM 11 O O2' C2E . . . E 2 86.383 -10.949 30.266 1 43.35 ? O2' C2E 801 A 1 HETATM 12 C C1' C2E . . . E 2 84.449 -10.632 31.345 1 44.69 ? C1' C2E 801 A 1 HETATM 13 N N9 C2E . . . E 2 83.074 -10.006 31.155 1 46.35 ? N9 C2E 801 A 1 HETATM 14 C C8 C2E . . . E 2 82.204 -9.11 31.669 1 47.65 ? C8 C2E 801 A 1 HETATM 15 N N7 C2E . . . E 2 81.099 -9.103 30.89 1 46.93 ? N7 C2E 801 A 1 HETATM 16 C C5 C2E . . . E 2 81.282 -9.985 29.908 1 45.72 ? C5 C2E 801 A 1 HETATM 17 C C6 C2E . . . E 2 80.384 -10.409 28.734 1 41.53 ? C6 C2E 801 A 1 HETATM 18 O O6 C2E . . . E 2 79.314 -9.913 28.598 1 39.92 ? O6 C2E 801 A 1 HETATM 19 N N1 C2E . . . E 2 80.838 -11.402 27.806 1 42.92 ? N1 C2E 801 A 1 HETATM 20 C C2 C2E . . . E 2 82.141 -11.997 27.98 1 45.02 ? C2 C2E 801 A 1 HETATM 21 N N2 C2E . . . E 2 82.609 -13.01 27.034 1 44.67 ? N2 C2E 801 A 1 HETATM 22 N N3 C2E . . . E 2 82.994 -11.589 29.102 1 47.31 ? N3 C2E 801 A 1 HETATM 23 C C4 C2E . . . E 2 82.516 -10.553 30.07 1 47.8 ? C4 C2E 801 A 1 HETATM 24 P P11 C2E . . . E 2 87.364 -7.411 29.952 1 44.49 ? P11 C2E 801 A 1 HETATM 25 O O21 C2E . . . E 2 88.701 -6.824 29.55 1 44.67 ? O21 C2E 801 A 1 HETATM 26 O O11 C2E . . . E 2 86.859 -8.153 28.733 1 44.68 ? O11 C2E 801 A 1 HETATM 27 O O5A C2E . . . E 2 86.16 -6.335 30.43 1 44.44 ? O5A C2E 801 A 1 HETATM 28 C C5A C2E . . . E 2 86.754 -5.288 31.179 1 44.86 ? C5A C2E 801 A 1 HETATM 29 C C4A C2E . . . E 2 85.828 -4.131 31.281 1 44.1 ? C4A C2E 801 A 1 HETATM 30 O O4A C2E . . . E 2 85.497 -3.685 30.106 1 46.38 ? O4A C2E 801 A 1 HETATM 31 C C3A C2E . . . E 2 84.359 -4.595 31.956 1 43.23 ? C3A C2E 801 A 1 HETATM 32 O O3A C2E . . . E 2 84.535 -4.836 33.441 1 49.79 ? O3A C2E 801 A 1 HETATM 33 C C2A C2E . . . E 2 83.602 -3.66 31.726 1 41.76 ? C2A C2E 801 A 1 HETATM 34 O O2A C2E . . . E 2 83.633 -2.67 32.866 1 41.75 ? O2A C2E 801 A 1 HETATM 35 C C1A C2E . . . E 2 84.189 -2.968 30.373 1 41.86 ? C1A C2E 801 A 1 HETATM 36 N N91 C2E . . . E 2 83.279 -2.979 29.395 1 41.1 ? N91 C2E 801 A 1 HETATM 37 C C81 C2E . . . E 2 83.885 -4.048 28.826 1 42.73 ? C81 C2E 801 A 1 HETATM 38 N N71 C2E . . . E 2 83.185 -4.374 27.716 1 42.34 ? N71 C2E 801 A 1 HETATM 39 C C51 C2E . . . E 2 82.165 -3.522 27.607 1 43.68 ? C51 C2E 801 A 1 HETATM 40 C C61 C2E . . . E 2 81.041 -3.39 26.57 1 54.77 ? C61 C2E 801 A 1 HETATM 41 O O61 C2E . . . E 2 80.979 -4.142 25.651 1 59.47 ? O61 C2E 801 A 1 HETATM 42 N N11 C2E . . . E 2 80.065 -2.354 26.715 1 56.63 ? N11 C2E 801 A 1 HETATM 43 C C21 C2E . . . E 2 80.13 -1.438 27.826 1 47.29 ? C21 C2E 801 A 1 HETATM 44 N N21 C2E . . . E 2 79.126 -0.383 27.966 1 51.63 ? N21 C2E 801 A 1 HETATM 45 N N31 C2E . . . E 2 81.204 -1.569 28.811 1 40.27 ? N31 C2E 801 A 1 HETATM 46 C C41 C2E . . . E 2 82.223 -2.649 28.66 1 40.25 ? C41 C2E 801 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 64 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #