data_5EXX # _model_server_result.job_id 0ofRcFkhTtOxWOC57dP0Bw _model_server_result.datetime_utc '2024-11-28 05:47:35' _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 5exx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 5EXX # _exptl.entry_id 5EXX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 3 _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 120 _cell.entry_id 5EXX _cell.length_a 137.836 _cell.length_b 137.836 _cell.length_c 172.773 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EXX _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 137.836 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 68.918 119.369478 0 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 68.918 119.369478 86.3865 5 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 137.836 0 86.3865 6 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 86.3865 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 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 5EXX _atom_sites.fract_transf_matrix[1][1] 0.007255 _atom_sites.fract_transf_matrix[1][2] 0.004189 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008377 _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] 0.005788 _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 SO4 A 1 501 1 SO4 SO4 . C 3 C2E A 1 502 360 C2E C2E . D 3 C2E A 1 503 361 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 . . . D 3 57.554 54.077 57.934 1 39.47 ? P1 C2E 503 A 1 HETATM 2 O O2P C2E . . . D 3 56.185 54.388 57.576 1 38.66 ? O2P C2E 503 A 1 HETATM 3 O O1P C2E . . . D 3 58.427 53.591 56.896 1 39.84 ? O1P C2E 503 A 1 HETATM 4 O O5' C2E . . . D 3 57.535 53.108 59.131 1 37.33 ? O5' C2E 503 A 1 HETATM 5 C C5' C2E . . . D 3 56.936 51.837 59.063 1 34.23 ? C5' C2E 503 A 1 HETATM 6 C C4' C2E . . . D 3 57.169 51.127 60.392 1 34.77 ? C4' C2E 503 A 1 HETATM 7 O O4' C2E . . . D 3 57.091 49.736 60.195 1 34.81 ? O4' C2E 503 A 1 HETATM 8 C C3' C2E . . . D 3 58.546 51.375 60.931 1 33.46 ? C3' C2E 503 A 1 HETATM 9 O O3' C2E . . . D 3 58.534 51.945 62.184 1 32.5 ? O3' C2E 503 A 1 HETATM 10 C C2' C2E . . . D 3 59.159 50.084 61.227 1 32.71 ? C2' C2E 503 A 1 HETATM 11 O O2' C2E . . . D 3 59.138 50.046 62.631 1 29.93 ? O2' C2E 503 A 1 HETATM 12 C C1' C2E . . . D 3 58.313 49.109 60.498 1 33.21 ? C1' C2E 503 A 1 HETATM 13 N N9 C2E . . . D 3 59.088 49.033 59.264 1 33.23 ? N9 C2E 503 A 1 HETATM 14 C C8 C2E . . . D 3 58.895 49.745 58.182 1 32.27 ? C8 C2E 503 A 1 HETATM 15 N N7 C2E . . . D 3 59.795 49.452 57.242 1 32.15 ? N7 C2E 503 A 1 HETATM 16 C C5 C2E . . . D 3 60.588 48.54 57.738 1 30.63 ? C5 C2E 503 A 1 HETATM 17 C C6 C2E . . . D 3 61.735 47.804 57.27 1 32.06 ? C6 C2E 503 A 1 HETATM 18 O O6 C2E . . . D 3 62.156 48.001 56.142 1 30.8 ? O6 C2E 503 A 1 HETATM 19 N N1 C2E . . . D 3 62.297 46.948 58.08 1 33.76 ? N1 C2E 503 A 1 HETATM 20 C C2 C2E . . . D 3 61.835 46.749 59.295 1 32.72 ? C2 C2E 503 A 1 HETATM 21 N N2 C2E . . . D 3 62.432 45.865 60.093 1 33.31 ? N2 C2E 503 A 1 HETATM 22 N N3 C2E . . . D 3 60.786 47.386 59.784 1 32.21 ? N3 C2E 503 A 1 HETATM 23 C C4 C2E . . . D 3 60.134 48.285 59.064 1 32.1 ? C4 C2E 503 A 1 HETATM 24 P P11 C2E . . . D 3 59.8 52.75 62.501 1 31.65 ? P11 C2E 503 A 1 HETATM 25 O O21 C2E . . . D 3 60.906 51.843 62.284 1 27.55 ? O21 C2E 503 A 1 HETATM 26 O O11 C2E . . . D 3 59.741 53.441 63.776 1 29.5 ? O11 C2E 503 A 1 HETATM 27 O O5A C2E . . . D 3 59.598 53.815 61.392 1 33.18 ? O5A C2E 503 A 1 HETATM 28 C C5A C2E . . . D 3 60.386 54.961 61.416 1 36.24 ? C5A C2E 503 A 1 HETATM 29 C C4A C2E . . . D 3 59.912 55.865 60.311 1 38.33 ? C4A C2E 503 A 1 HETATM 30 O O4A C2E . . . D 3 61.016 56.686 60.048 1 37.57 ? O4A C2E 503 A 1 HETATM 31 C C3A C2E . . . D 3 59.571 55.144 59.033 1 38.77 ? C3A C2E 503 A 1 HETATM 32 O O3A C2E . . . D 3 58.246 55.301 58.616 1 38.66 ? O3A C2E 503 A 1 HETATM 33 C C2A C2E . . . D 3 60.3 55.931 58.024 1 40.64 ? C2A C2E 503 A 1 HETATM 34 O O2A C2E . . . D 3 59.489 57.062 57.857 1 42.02 ? O2A C2E 503 A 1 HETATM 35 C C1A C2E . . . D 3 61.482 56.452 58.749 1 40.16 ? C1A C2E 503 A 1 HETATM 36 N N91 C2E . . . D 3 62.601 55.512 58.872 1 40.38 ? N91 C2E 503 A 1 HETATM 37 C C81 C2E . . . D 3 62.723 54.608 59.815 1 40.15 ? C81 C2E 503 A 1 HETATM 38 N N71 C2E . . . D 3 63.868 53.941 59.691 1 38.09 ? N71 C2E 503 A 1 HETATM 39 C C51 C2E . . . D 3 64.5 54.43 58.661 1 40.42 ? C51 C2E 503 A 1 HETATM 40 C C61 C2E . . . D 3 65.746 54.146 58.019 1 40.53 ? C61 C2E 503 A 1 HETATM 41 O O61 C2E . . . D 3 66.462 53.265 58.472 1 40.64 ? O61 C2E 503 A 1 HETATM 42 N N11 C2E . . . D 3 66.07 54.847 56.968 1 42.18 ? N11 C2E 503 A 1 HETATM 43 C C21 C2E . . . D 3 65.288 55.788 56.506 1 42.97 ? C21 C2E 503 A 1 HETATM 44 N N21 C2E . . . D 3 65.674 56.465 55.438 1 45.13 ? N21 C2E 503 A 1 HETATM 45 N N31 C2E . . . D 3 64.126 56.1 57.048 1 43.2 ? N31 C2E 503 A 1 HETATM 46 C C41 C2E . . . D 3 63.677 55.459 58.12 1 41.52 ? C41 C2E 503 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 46 #