data_3GFY # _model_server_result.job_id C1vUq6KgseCAyaJ7y6s44A _model_server_result.datetime_utc '2025-03-04 17:23:20' _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 3gfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 3GFY # _exptl.entry_id 3GFY _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 3GFY _cell.length_a 68.43 _cell.length_b 96.53 _cell.length_c 127.07 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GFY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,H _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 C N N ? 2 E 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 3GFY _atom_sites.fract_transf_matrix[1][1] 0.014613 _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] 0.010359 _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] 0.00787 _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 1 501 501 C2E C2E . D 3 FMN A 1 504 504 FMN FMN . E 2 C2E B 1 501 501 C2E C2E . F 3 FMN B 1 504 504 FMN FMN . G 4 HOH A 1 406 7 HOH HOH . G 4 HOH A 2 407 15 HOH HOH . G 4 HOH A 3 408 22 HOH HOH . G 4 HOH A 4 409 23 HOH HOH . G 4 HOH A 5 410 26 HOH HOH . G 4 HOH A 6 411 32 HOH HOH . G 4 HOH A 7 412 34 HOH HOH . G 4 HOH A 8 413 35 HOH HOH . G 4 HOH A 9 414 40 HOH HOH . G 4 HOH A 10 415 47 HOH HOH . G 4 HOH A 11 416 49 HOH HOH . G 4 HOH A 12 417 51 HOH HOH . G 4 HOH A 13 418 56 HOH HOH . G 4 HOH A 14 419 57 HOH HOH . G 4 HOH A 15 420 58 HOH HOH . G 4 HOH A 16 421 65 HOH HOH . G 4 HOH A 17 422 71 HOH HOH . G 4 HOH A 18 423 72 HOH HOH . G 4 HOH A 19 424 73 HOH HOH . G 4 HOH A 20 425 75 HOH HOH . H 4 HOH B 1 406 1 HOH HOH . H 4 HOH B 2 407 6 HOH HOH . H 4 HOH B 3 408 12 HOH HOH . H 4 HOH B 4 409 18 HOH HOH . H 4 HOH B 5 410 24 HOH HOH . H 4 HOH B 6 411 25 HOH HOH . H 4 HOH B 7 412 27 HOH HOH . H 4 HOH B 8 413 28 HOH HOH . H 4 HOH B 9 414 29 HOH HOH . H 4 HOH B 10 415 30 HOH HOH . H 4 HOH B 11 416 31 HOH HOH . H 4 HOH B 12 417 36 HOH HOH . H 4 HOH B 13 418 37 HOH HOH . H 4 HOH B 14 419 38 HOH HOH . H 4 HOH B 15 420 42 HOH HOH . H 4 HOH B 16 421 43 HOH HOH . H 4 HOH B 17 422 44 HOH HOH . H 4 HOH B 18 423 45 HOH HOH . H 4 HOH B 19 424 46 HOH HOH . H 4 HOH B 20 425 50 HOH HOH . H 4 HOH B 21 426 53 HOH HOH . H 4 HOH B 22 427 55 HOH HOH . H 4 HOH B 23 428 61 HOH HOH . H 4 HOH B 24 429 62 HOH HOH . H 4 HOH B 25 430 63 HOH HOH . H 4 HOH B 26 431 64 HOH HOH . H 4 HOH B 27 432 66 HOH HOH . H 4 HOH B 28 433 67 HOH HOH . H 4 HOH B 29 434 70 HOH HOH . H 4 HOH B 30 435 74 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 -24.189 -2.724 -1.068 1 19.62 ? P1 C2E 501 A 1 HETATM 2 O O2P C2E . . . C 2 -23.287 -3.871 -0.705 1 19.93 ? O2P C2E 501 A 1 HETATM 3 O O1P C2E . . . C 2 -23.545 -1.471 -1.61 1 20.6 ? O1P C2E 501 A 1 HETATM 4 O O5' C2E . . . C 2 -25.21 -3.172 -2.225 1 19.59 ? O5' C2E 501 A 1 HETATM 5 C C5' C2E . . . C 2 -26.052 -4.31 -2.147 1 17.95 ? C5' C2E 501 A 1 HETATM 6 C C4' C2E . . . C 2 -27.48 -3.802 -2.023 1 17.22 ? C4' C2E 501 A 1 HETATM 7 O O4' C2E . . . C 2 -27.937 -3.281 -3.27 1 16.29 ? O4' C2E 501 A 1 HETATM 8 C C3' C2E . . . C 2 -28.424 -4.936 -1.667 1 16.43 ? C3' C2E 501 A 1 HETATM 9 O O3' C2E . . . C 2 -29.382 -4.434 -0.753 1 16.49 ? O3' C2E 501 A 1 HETATM 10 C C2' C2E . . . C 2 -29.129 -5.227 -2.941 1 15.95 ? C2' C2E 501 A 1 HETATM 11 O O2' C2E . . . C 2 -30.273 -5.907 -2.9 1 15.46 ? O2' C2E 501 A 1 HETATM 12 C C1' C2E . . . C 2 -28.968 -4.189 -3.753 1 15.58 ? C1' C2E 501 A 1 HETATM 13 N N9 C2E . . . C 2 -29.094 -4.313 -5.099 1 15.31 ? N9 C2E 501 A 1 HETATM 14 C C8 C2E . . . C 2 -28.455 -5.174 -5.797 1 15.16 ? C8 C2E 501 A 1 HETATM 15 N N7 C2E . . . C 2 -28.788 -5.003 -7.025 1 15.27 ? N7 C2E 501 A 1 HETATM 16 C C5 C2E . . . C 2 -29.667 -3.982 -7.138 1 15.07 ? C5 C2E 501 A 1 HETATM 17 C C6 C2E . . . C 2 -30.337 -3.374 -8.186 1 15.17 ? C6 C2E 501 A 1 HETATM 18 O O6 C2E . . . C 2 -30.176 -3.771 -9.362 1 15.19 ? O6 C2E 501 A 1 HETATM 19 N N1 C2E . . . C 2 -31.168 -2.343 -7.908 1 15 ? N1 C2E 501 A 1 HETATM 20 C C2 C2E . . . C 2 -31.344 -1.908 -6.636 1 14.97 ? C2 C2E 501 A 1 HETATM 21 N N2 C2E . . . C 2 -32.18 -0.875 -6.404 1 15.09 ? N2 C2E 501 A 1 HETATM 22 N N3 C2E . . . C 2 -30.7 -2.485 -5.595 1 14.87 ? N3 C2E 501 A 1 HETATM 23 C C4 C2E . . . C 2 -29.863 -3.519 -5.839 1 14.97 ? C4 C2E 501 A 1 HETATM 24 P P11 C2E . . . C 2 -29.186 -4.697 0.811 1 15.84 ? P11 C2E 501 A 1 HETATM 25 O O21 C2E . . . C 2 -30.648 -4.592 1.461 1 15.97 ? O21 C2E 501 A 1 HETATM 26 O O11 C2E . . . C 2 -28.772 -6.239 0.99 1 16.07 ? O11 C2E 501 A 1 HETATM 27 O O5A C2E . . . C 2 -27.901 -3.913 1.385 1 16.4 ? O5A C2E 501 A 1 HETATM 28 C C5A C2E . . . C 2 -27.958 -2.634 2.005 1 16.88 ? C5A C2E 501 A 1 HETATM 29 C C4A C2E . . . C 2 -26.466 -2.387 2.223 1 17.5 ? C4A C2E 501 A 1 HETATM 30 O O4A C2E . . . C 2 -26.091 -2.773 3.55 1 17.82 ? O4A C2E 501 A 1 HETATM 31 C C3A C2E . . . C 2 -25.498 -3.118 1.285 1 18.44 ? C3A C2E 501 A 1 HETATM 32 O O3A C2E . . . C 2 -25.133 -2.298 0.174 1 19.55 ? O3A C2E 501 A 1 HETATM 33 C C2A C2E . . . C 2 -24.331 -3.405 2.179 1 18.56 ? C2A C2E 501 A 1 HETATM 34 O O2A C2E . . . C 2 -23.625 -2.286 2.311 1 19.34 ? O2A C2E 501 A 1 HETATM 35 C C1A C2E . . . C 2 -24.967 -3.649 3.317 1 18.29 ? C1A C2E 501 A 1 HETATM 36 N N91 C2E . . . C 2 -24.646 -4.729 4.084 1 18.04 ? N91 C2E 501 A 1 HETATM 37 C C81 C2E . . . C 2 -25.111 -5.927 3.747 1 17.99 ? C81 C2E 501 A 1 HETATM 38 N N71 C2E . . . C 2 -24.596 -6.771 4.666 1 18.25 ? N71 C2E 501 A 1 HETATM 39 C C51 C2E . . . C 2 -23.826 -6.06 5.526 1 18.08 ? C51 C2E 501 A 1 HETATM 40 C C61 C2E . . . C 2 -23.08 -6.432 6.633 1 18.18 ? C61 C2E 501 A 1 HETATM 41 O O61 C2E . . . C 2 -23.042 -7.63 6.994 1 17.95 ? O61 C2E 501 A 1 HETATM 42 N N11 C2E . . . C 2 -22.395 -5.485 7.31 1 18.15 ? N11 C2E 501 A 1 HETATM 43 C C21 C2E . . . C 2 -22.425 -4.188 6.93 1 18.18 ? C21 C2E 501 A 1 HETATM 44 N N21 C2E . . . C 2 -21.719 -3.288 7.654 1 18.2 ? N21 C2E 501 A 1 HETATM 45 N N31 C2E . . . C 2 -23.148 -3.795 5.846 1 18.36 ? N31 C2E 501 A 1 HETATM 46 C C41 C2E . . . C 2 -23.847 -4.725 5.143 1 18.11 ? C41 C2E 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #