data_8PFA # _model_server_result.job_id xyxuLt23Lx-zUFb6Y258Xw _model_server_result.datetime_utc '2025-07-09 23:39:24' _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 8pfa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":350}' # _entry.id 8PFA # _exptl.entry_id 8PFA _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 120 _cell.entry_id 8PFA _cell.length_a 108.165 _cell.length_b 108.165 _cell.length_c 87.446 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PFA _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall 'R 3' _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 J 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 76 n n O1P P1 C2E doub 77 n n O5' P1 C2E sing 78 n n C5' O5' C2E sing 79 n n C4' O4' C2E sing 80 n n C4' C5' C2E sing 81 n n C3' C4' C2E sing 82 n n O3' P11 C2E sing 83 n n O3' C3' C2E sing 84 n n C2' C3' C2E sing 85 n n C2' C1' C2E sing 86 n n O2' C2' C2E sing 87 n n C1' O4' C2E sing 88 n n C1' N9 C2E sing 89 n n N9 C4 C2E sing 90 n y N9 C8 C2E sing 91 n y C8 N7 C2E doub 92 n y C5 N7 C2E sing 93 n y C5 C6 C2E sing 94 n n C6 O6 C2E doub 95 n n N1 C6 C2E sing 96 n n C2 N1 C2E sing 97 n n N2 C2 C2E sing 98 n n N3 C2 C2E doub 99 n n N3 C4 C2E sing 100 n n C4 C5 C2E doub 101 n y P11 O21 C2E sing 102 n n P11 O5A C2E sing 103 n n O11 P11 C2E doub 104 n n C5A O5A C2E sing 105 n n C5A C4A C2E sing 106 n n C4A O4A C2E sing 107 n n C4A C3A C2E sing 108 n n O4A C1A C2E sing 109 n n C3A C2A C2E sing 110 n n O3A C3A C2E sing 111 n n O3A P1 C2E sing 112 n n C2A O2A C2E sing 113 n n C1A C2A C2E sing 114 n n C1A N91 C2E sing 115 n n N91 C41 C2E sing 116 n y C81 N71 C2E doub 117 n y C81 N91 C2E sing 118 n y N71 C51 C2E sing 119 n y C51 C41 C2E doub 120 n y C51 C61 C2E sing 121 n n C61 O61 C2E doub 122 n n C61 N11 C2E sing 123 n n C21 N11 C2E sing 124 n n C21 N21 C2E sing 125 n n N31 C21 C2E doub 126 n n C41 N31 C2E sing 127 n n O2P HO2P C2E sing 128 n n C5' "H5'1" C2E sing 129 n n C5' "H5'2" C2E sing 130 n n C4' H4' C2E sing 131 n n C3' H3' C2E sing 132 n n C2' H2' C2E sing 133 n n O2' HO2' C2E sing 134 n n C1' H1' C2E sing 135 n n C8 H8 C2E sing 136 n n N1 HN1 C2E sing 137 n n N2 HN21 C2E sing 138 n n N2 HN22 C2E sing 139 n n O21 HO21 C2E sing 140 n n C5A H511 C2E sing 141 n n C5A H512 C2E sing 142 n n C4A H4A C2E sing 143 n n C3A H3A C2E sing 144 n n C2A H2A C2E sing 145 n n O2A HO2A C2E sing 146 n n C1A H1A C2E sing 147 n n C81 H81 C2E sing 148 n n N11 HN11 C2E sing 149 n n N21 HN24 C2E sing 150 n n N21 HN23 C2E sing 151 n n # _atom_sites.entry_id 8PFA _atom_sites.fract_transf_matrix[1][1] 0.009245 _atom_sites.fract_transf_matrix[1][2] 0.005338 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010675 _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] 0.011436 _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 1 350 150 C2E C2E . D 3 SO4 A 1 351 1 SO4 SO4 . E 3 SO4 A 1 352 10 SO4 SO4 . F 3 SO4 A 1 353 12 SO4 SO4 . G 4 ACT A 1 354 4 ACT ACT . H 4 ACT A 1 355 5 ACT ACT . I 4 ACT A 1 356 6 ACT ACT . J 2 C2E B 1 350 150 C2E C2E . K 3 SO4 B 1 351 2 SO4 SO4 . L 3 SO4 B 1 352 3 SO4 SO4 . M 3 SO4 B 1 353 6 SO4 SO4 . N 3 SO4 B 1 354 7 SO4 SO4 . O 3 SO4 B 1 355 8 SO4 SO4 . P 3 SO4 B 1 356 9 SO4 SO4 . Q 3 SO4 B 1 357 11 SO4 SO4 . R 4 ACT B 1 358 10 ACT ACT . S 4 ACT B 1 359 11 ACT ACT . T 5 HOH A 1 400 57 HOH HOH . T 5 HOH A 2 401 12 HOH HOH . T 5 HOH A 3 402 96 HOH HOH . T 5 HOH A 4 403 5 HOH HOH . T 5 HOH A 5 404 49 HOH HOH . T 5 HOH A 6 405 6 HOH HOH . T 5 HOH A 7 406 78 HOH HOH . T 5 HOH A 8 407 28 HOH HOH . T 5 HOH A 9 408 13 HOH HOH . T 5 HOH A 10 409 72 HOH HOH . T 5 HOH A 11 410 3 HOH HOH . T 5 HOH A 12 411 92 HOH HOH . T 5 HOH A 13 412 39 HOH HOH . T 5 HOH A 14 413 51 HOH HOH . T 5 HOH A 15 414 45 HOH HOH . T 5 HOH A 16 415 47 HOH HOH . T 5 HOH A 17 416 43 HOH HOH . T 5 HOH A 18 417 84 HOH HOH . T 5 HOH A 19 418 15 HOH HOH . T 5 HOH A 20 419 2 HOH HOH . T 5 HOH A 21 420 29 HOH HOH . T 5 HOH A 22 421 14 HOH HOH . T 5 HOH A 23 422 77 HOH HOH . T 5 HOH A 24 423 42 HOH HOH . T 5 HOH A 25 424 7 HOH HOH . T 5 HOH A 26 425 30 HOH HOH . T 5 HOH A 27 426 4 HOH HOH . T 5 HOH A 28 427 1 HOH HOH . T 5 HOH A 29 428 85 HOH HOH . T 5 HOH A 30 429 62 HOH HOH . T 5 HOH A 31 430 65 HOH HOH . T 5 HOH A 32 431 10 HOH HOH . T 5 HOH A 33 432 60 HOH HOH . T 5 HOH A 34 433 59 HOH HOH . T 5 HOH A 35 434 52 HOH HOH . T 5 HOH A 36 435 22 HOH HOH . T 5 HOH A 37 436 71 HOH HOH . T 5 HOH A 38 437 66 HOH HOH . T 5 HOH A 39 438 67 HOH HOH . T 5 HOH A 40 439 38 HOH HOH . T 5 HOH A 41 440 87 HOH HOH . T 5 HOH A 42 441 41 HOH HOH . T 5 HOH A 43 442 94 HOH HOH . T 5 HOH A 44 443 36 HOH HOH . T 5 HOH A 45 444 69 HOH HOH . T 5 HOH A 46 445 86 HOH HOH . T 5 HOH A 47 446 54 HOH HOH . T 5 HOH A 48 447 50 HOH HOH . T 5 HOH A 49 448 91 HOH HOH . T 5 HOH A 50 449 17 HOH HOH . T 5 HOH A 51 450 90 HOH HOH . T 5 HOH A 52 451 75 HOH HOH . T 5 HOH A 53 452 70 HOH HOH . U 5 HOH B 1 400 68 HOH HOH . U 5 HOH B 2 401 31 HOH HOH . U 5 HOH B 3 402 82 HOH HOH . U 5 HOH B 4 403 58 HOH HOH . U 5 HOH B 5 404 8 HOH HOH . U 5 HOH B 6 405 27 HOH HOH . U 5 HOH B 7 406 32 HOH HOH . U 5 HOH B 8 407 21 HOH HOH . U 5 HOH B 9 408 9 HOH HOH . U 5 HOH B 10 409 26 HOH HOH . U 5 HOH B 11 410 20 HOH HOH . U 5 HOH B 12 411 37 HOH HOH . U 5 HOH B 13 412 44 HOH HOH . U 5 HOH B 14 413 53 HOH HOH . U 5 HOH B 15 414 33 HOH HOH . U 5 HOH B 16 415 48 HOH HOH . U 5 HOH B 17 416 55 HOH HOH . U 5 HOH B 18 417 19 HOH HOH . U 5 HOH B 19 418 24 HOH HOH . U 5 HOH B 20 419 25 HOH HOH . U 5 HOH B 21 420 11 HOH HOH . U 5 HOH B 22 421 18 HOH HOH . U 5 HOH B 23 422 46 HOH HOH . U 5 HOH B 24 423 16 HOH HOH . U 5 HOH B 25 424 83 HOH HOH . U 5 HOH B 26 425 95 HOH HOH . U 5 HOH B 27 426 81 HOH HOH . U 5 HOH B 28 427 34 HOH HOH . U 5 HOH B 29 428 73 HOH HOH . U 5 HOH B 30 429 88 HOH HOH . U 5 HOH B 31 430 23 HOH HOH . U 5 HOH B 32 431 64 HOH HOH . U 5 HOH B 33 432 63 HOH HOH . U 5 HOH B 34 433 35 HOH HOH . U 5 HOH B 35 434 74 HOH HOH . U 5 HOH B 36 435 76 HOH HOH . U 5 HOH B 37 436 40 HOH HOH . U 5 HOH B 38 437 89 HOH HOH . U 5 HOH B 39 438 80 HOH HOH . U 5 HOH B 40 439 93 HOH HOH . U 5 HOH B 41 440 56 HOH HOH . U 5 HOH B 42 441 61 HOH HOH . U 5 HOH B 43 442 79 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 . . . J 2 -31.922 -43.086 24.148 1 54.85 ? P1 C2E 350 B 1 HETATM 2 O O2P C2E . . . J 2 -30.549 -42.868 24.747 1 54.55 ? O2P C2E 350 B 1 HETATM 3 O O1P C2E . . . J 2 -32.895 -43.276 25.272 1 53.99 -1 O1P C2E 350 B 1 HETATM 4 O O5' C2E . . . J 2 -32.486 -41.784 23.337 1 51.42 ? O5' C2E 350 B 1 HETATM 5 C C5' C2E . . . J 2 -33.801 -41.862 22.751 1 50.79 ? C5' C2E 350 B 1 HETATM 6 C C4' C2E . . . J 2 -33.86 -40.652 21.747 1 51.54 ? C4' C2E 350 B 1 HETATM 7 O O4' C2E . . . J 2 -33.825 -39.565 22.464 1 46.76 ? O4' C2E 350 B 1 HETATM 8 C C3' C2E . . . J 2 -32.6 -40.659 20.876 1 52.94 ? C3' C2E 350 B 1 HETATM 9 O O3' C2E . . . J 2 -32.945 -41.194 19.685 1 49.9 ? O3' C2E 350 B 1 HETATM 10 C C2' C2E . . . J 2 -32.24 -39.157 20.73 1 57.22 ? C2' C2E 350 B 1 HETATM 11 O O2' C2E . . . J 2 -33.025 -38.604 19.566 1 56.42 ? O2' C2E 350 B 1 HETATM 12 C C1' C2E . . . J 2 -32.772 -38.582 21.759 1 48.11 ? C1' C2E 350 B 1 HETATM 13 N N9 C2E . . . J 2 -32.015 -38.034 22.877 1 46.21 ? N9 C2E 350 B 1 HETATM 14 C C8 C2E . . . J 2 -30.951 -38.878 23.038 1 44.37 ? C8 C2E 350 B 1 HETATM 15 N N7 C2E . . . J 2 -30.212 -38.412 24.106 1 43.14 ? N7 C2E 350 B 1 HETATM 16 C C5 C2E . . . J 2 -30.842 -37.327 24.59 1 46.84 ? C5 C2E 350 B 1 HETATM 17 C C6 C2E . . . J 2 -30.633 -36.31 25.723 1 46.74 ? C6 C2E 350 B 1 HETATM 18 O O6 C2E . . . J 2 -29.705 -36.352 26.466 1 51.44 ? O6 C2E 350 B 1 HETATM 19 N N1 C2E . . . J 2 -31.579 -35.273 25.901 1 47.71 ? N1 C2E 350 B 1 HETATM 20 C C2 C2E . . . J 2 -32.72 -35.142 25.03 1 44.43 ? C2 C2E 350 B 1 HETATM 21 N N2 C2E . . . J 2 -33.705 -34.111 25.162 1 50.48 ? N2 C2E 350 B 1 HETATM 22 N N3 C2E . . . J 2 -32.904 -36.077 23.976 1 45.43 ? N3 C2E 350 B 1 HETATM 23 C C4 C2E . . . J 2 -31.946 -37.154 23.809 1 40.12 ? C4 C2E 350 B 1 HETATM 24 P P11 C2E . . . J 2 -31.631 -41.934 18.858 1 57.59 ? P11 C2E 350 B 1 HETATM 25 O O21 C2E . . . J 2 -30.457 -41.035 18.511 1 66.82 ? O21 C2E 350 B 1 HETATM 26 O O11 C2E . . . J 2 -32.147 -42.449 17.548 1 58.9 -1 O11 C2E 350 B 1 HETATM 27 O O5A C2E . . . J 2 -31.204 -43.267 19.888 1 58.06 ? O5A C2E 350 B 1 HETATM 28 C C5A C2E . . . J 2 -32.197 -44.285 20.01 1 55.77 ? C5A C2E 350 B 1 HETATM 29 C C4A C2E . . . J 2 -31.537 -45.327 20.857 1 56.45 ? C4A C2E 350 B 1 HETATM 30 O O4A C2E . . . J 2 -30.508 -45.82 20.229 1 57.7 ? O4A C2E 350 B 1 HETATM 31 C C3A C2E . . . J 2 -30.904 -44.57 22.201 1 51.11 ? C3A C2E 350 B 1 HETATM 32 O O3A C2E . . . J 2 -31.982 -44.568 23.274 1 55.84 ? O3A C2E 350 B 1 HETATM 33 C C2A C2E . . . J 2 -29.899 -45.203 22.536 1 55.89 ? C2A C2E 350 B 1 HETATM 34 O O2A C2E . . . J 2 -30.275 -46.33 23.467 1 63.71 ? O2A C2E 350 B 1 HETATM 35 C C1A C2E . . . J 2 -29.325 -45.85 21.174 1 56.37 ? C1A C2E 350 B 1 HETATM 36 N N91 C2E . . . J 2 -28.367 -45.154 20.598 1 63.93 ? N91 C2E 350 B 1 HETATM 37 C C81 C2E . . . J 2 -28.187 -43.81 20.422 1 62.93 ? C81 C2E 350 B 1 HETATM 38 N N71 C2E . . . J 2 -27.035 -43.66 19.71 1 62.07 ? N71 C2E 350 B 1 HETATM 39 C C51 C2E . . . J 2 -26.542 -44.882 19.44 1 56.58 ? C51 C2E 350 B 1 HETATM 40 C C61 C2E . . . J 2 -25.288 -45.338 18.677 1 57.49 ? C61 C2E 350 B 1 HETATM 41 O O61 C2E . . . J 2 -24.559 -44.569 18.189 1 56.1 ? O61 C2E 350 B 1 HETATM 42 N N11 C2E . . . J 2 -25.002 -46.75 18.534 1 60.94 ? N11 C2E 350 B 1 HETATM 43 C C21 C2E . . . J 2 -25.889 -47.724 19.121 1 59.6 ? C21 C2E 350 B 1 HETATM 44 N N21 C2E . . . J 2 -25.586 -49.184 18.975 1 64.71 ? N21 C2E 350 B 1 HETATM 45 N N31 C2E . . . J 2 -27.091 -47.284 19.856 1 61.5 ? N31 C2E 350 B 1 HETATM 46 C C41 C2E . . . J 2 -27.386 -45.818 19.994 1 53.14 ? C41 C2E 350 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 46 #