data_8PE0 # _model_server_result.job_id -qs200ClvpxLZDWEPshcJg _model_server_result.datetime_utc '2025-07-15 08:15:00' _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 8pe0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":350}' # _entry.id 8PE0 # _exptl.entry_id 8PE0 _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 8PE0 _cell.length_a 108.434 _cell.length_b 108.434 _cell.length_c 88.125 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PE0 _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,V,W,X,Y,Z _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 N 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 8PE0 _atom_sites.fract_transf_matrix[1][1] 0.009222 _atom_sites.fract_transf_matrix[1][2] 0.005324 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010649 _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] 0.011348 _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 4 SO4 SO4 . F 3 SO4 A 1 353 7 SO4 SO4 . G 4 ACT A 1 354 1 ACT ACT . H 4 ACT A 1 355 5 ACT ACT . I 4 ACT A 1 356 8 ACT ACT . J 4 ACT A 1 357 10 ACT ACT . K 4 ACT A 1 358 12 ACT ACT . L 4 ACT A 1 359 13 ACT ACT . M 4 ACT A 1 360 14 ACT ACT . N 2 C2E B 1 350 150 C2E C2E . O 3 SO4 B 1 351 2 SO4 SO4 . P 3 SO4 B 1 352 5 SO4 SO4 . Q 3 SO4 B 1 353 6 SO4 SO4 . R 3 SO4 B 1 354 8 SO4 SO4 . S 4 ACT B 1 355 2 ACT ACT . T 4 ACT B 1 356 4 ACT ACT . U 4 ACT B 1 357 7 ACT ACT . V 4 ACT B 1 358 11 ACT ACT . W 4 ACT B 1 359 15 ACT ACT . X 4 ACT B 1 360 19 ACT ACT . Y 5 HOH A 1 400 96 HOH HOH . Y 5 HOH A 2 401 9 HOH HOH . Y 5 HOH A 3 402 76 HOH HOH . Y 5 HOH A 4 403 113 HOH HOH . Y 5 HOH A 5 404 19 HOH HOH . Y 5 HOH A 6 405 30 HOH HOH . Y 5 HOH A 7 406 8 HOH HOH . Y 5 HOH A 8 407 134 HOH HOH . Y 5 HOH A 9 408 12 HOH HOH . Y 5 HOH A 10 409 6 HOH HOH . Y 5 HOH A 11 410 55 HOH HOH . Y 5 HOH A 12 411 14 HOH HOH . Y 5 HOH A 13 412 15 HOH HOH . Y 5 HOH A 14 413 23 HOH HOH . Y 5 HOH A 15 414 132 HOH HOH . Y 5 HOH A 16 415 93 HOH HOH . Y 5 HOH A 17 416 39 HOH HOH . Y 5 HOH A 18 417 10 HOH HOH . Y 5 HOH A 19 418 98 HOH HOH . Y 5 HOH A 20 419 16 HOH HOH . Y 5 HOH A 21 420 18 HOH HOH . Y 5 HOH A 22 421 17 HOH HOH . Y 5 HOH A 23 422 70 HOH HOH . Y 5 HOH A 24 423 21 HOH HOH . Y 5 HOH A 25 424 20 HOH HOH . Y 5 HOH A 26 425 125 HOH HOH . Y 5 HOH A 27 426 87 HOH HOH . Y 5 HOH A 28 427 56 HOH HOH . Y 5 HOH A 29 428 25 HOH HOH . Y 5 HOH A 30 429 91 HOH HOH . Y 5 HOH A 31 430 1 HOH HOH . Y 5 HOH A 32 431 2 HOH HOH . Y 5 HOH A 33 432 31 HOH HOH . Y 5 HOH A 34 433 11 HOH HOH . Y 5 HOH A 35 434 63 HOH HOH . Y 5 HOH A 36 435 120 HOH HOH . Y 5 HOH A 37 436 110 HOH HOH . Y 5 HOH A 38 437 36 HOH HOH . Y 5 HOH A 39 438 5 HOH HOH . Y 5 HOH A 40 439 45 HOH HOH . Y 5 HOH A 41 440 51 HOH HOH . Y 5 HOH A 42 441 49 HOH HOH . Y 5 HOH A 43 442 44 HOH HOH . Y 5 HOH A 44 443 33 HOH HOH . Y 5 HOH A 45 444 71 HOH HOH . Y 5 HOH A 46 445 82 HOH HOH . Y 5 HOH A 47 446 32 HOH HOH . Y 5 HOH A 48 447 129 HOH HOH . Y 5 HOH A 49 448 99 HOH HOH . Y 5 HOH A 50 449 130 HOH HOH . Y 5 HOH A 51 450 105 HOH HOH . Y 5 HOH A 52 451 81 HOH HOH . Y 5 HOH A 53 452 142 HOH HOH . Y 5 HOH A 54 453 112 HOH HOH . Y 5 HOH A 55 454 13 HOH HOH . Y 5 HOH A 56 455 64 HOH HOH . Y 5 HOH A 57 456 94 HOH HOH . Y 5 HOH A 58 457 77 HOH HOH . Y 5 HOH A 59 458 79 HOH HOH . Y 5 HOH A 60 459 43 HOH HOH . Y 5 HOH A 61 460 26 HOH HOH . Y 5 HOH A 62 461 80 HOH HOH . Y 5 HOH A 63 462 34 HOH HOH . Y 5 HOH A 64 463 85 HOH HOH . Y 5 HOH A 65 464 100 HOH HOH . Y 5 HOH A 66 465 127 HOH HOH . Y 5 HOH A 67 466 111 HOH HOH . Y 5 HOH A 68 467 115 HOH HOH . Y 5 HOH A 69 468 117 HOH HOH . Y 5 HOH A 70 469 47 HOH HOH . Z 5 HOH B 1 400 40 HOH HOH . Z 5 HOH B 2 401 42 HOH HOH . Z 5 HOH B 3 402 46 HOH HOH . Z 5 HOH B 4 403 75 HOH HOH . Z 5 HOH B 5 404 68 HOH HOH . Z 5 HOH B 6 405 59 HOH HOH . Z 5 HOH B 7 406 65 HOH HOH . Z 5 HOH B 8 407 102 HOH HOH . Z 5 HOH B 9 408 144 HOH HOH . Z 5 HOH B 10 409 22 HOH HOH . Z 5 HOH B 11 410 37 HOH HOH . Z 5 HOH B 12 411 83 HOH HOH . Z 5 HOH B 13 412 72 HOH HOH . Z 5 HOH B 14 413 38 HOH HOH . Z 5 HOH B 15 414 126 HOH HOH . Z 5 HOH B 16 415 29 HOH HOH . Z 5 HOH B 17 416 74 HOH HOH . Z 5 HOH B 18 417 139 HOH HOH . Z 5 HOH B 19 418 7 HOH HOH . Z 5 HOH B 20 419 35 HOH HOH . Z 5 HOH B 21 420 48 HOH HOH . Z 5 HOH B 22 421 54 HOH HOH . Z 5 HOH B 23 422 28 HOH HOH . Z 5 HOH B 24 423 89 HOH HOH . Z 5 HOH B 25 424 73 HOH HOH . Z 5 HOH B 26 425 106 HOH HOH . Z 5 HOH B 27 426 107 HOH HOH . Z 5 HOH B 28 427 109 HOH HOH . Z 5 HOH B 29 428 3 HOH HOH . Z 5 HOH B 30 429 61 HOH HOH . Z 5 HOH B 31 430 4 HOH HOH . Z 5 HOH B 32 431 24 HOH HOH . Z 5 HOH B 33 432 114 HOH HOH . Z 5 HOH B 34 433 103 HOH HOH . Z 5 HOH B 35 434 97 HOH HOH . Z 5 HOH B 36 435 137 HOH HOH . Z 5 HOH B 37 436 62 HOH HOH . Z 5 HOH B 38 437 52 HOH HOH . Z 5 HOH B 39 438 86 HOH HOH . Z 5 HOH B 40 439 140 HOH HOH . Z 5 HOH B 41 440 57 HOH HOH . Z 5 HOH B 42 441 53 HOH HOH . Z 5 HOH B 43 442 133 HOH HOH . Z 5 HOH B 44 443 124 HOH HOH . Z 5 HOH B 45 444 66 HOH HOH . Z 5 HOH B 46 445 143 HOH HOH . Z 5 HOH B 47 446 69 HOH HOH . Z 5 HOH B 48 447 27 HOH HOH . Z 5 HOH B 49 448 88 HOH HOH . Z 5 HOH B 50 449 128 HOH HOH . Z 5 HOH B 51 450 122 HOH HOH . Z 5 HOH B 52 451 104 HOH HOH . Z 5 HOH B 53 452 108 HOH HOH . Z 5 HOH B 54 453 58 HOH HOH . Z 5 HOH B 55 454 90 HOH HOH . Z 5 HOH B 56 455 78 HOH HOH . Z 5 HOH B 57 456 60 HOH HOH . Z 5 HOH B 58 457 41 HOH HOH . Z 5 HOH B 59 458 67 HOH HOH . Z 5 HOH B 60 459 141 HOH HOH . Z 5 HOH B 61 460 95 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 2.15 -24.697 19.902 1 47.71 ? P1 C2E 350 A 1 HETATM 2 O O2P C2E . . . C 2 1.438 -25.676 19.005 1 48.18 ? O2P C2E 350 A 1 HETATM 3 O O1P C2E . . . C 2 2.972 -23.829 19.005 1 48.08 -1 O1P C2E 350 A 1 HETATM 4 O O5' C2E . . . C 2 1.139 -23.676 20.636 1 45.6 ? O5' C2E 350 A 1 HETATM 5 C C5' C2E . . . C 2 1.729 -22.613 21.406 1 46 ? C5' C2E 350 A 1 HETATM 6 C C4' C2E . . . C 2 0.553 -22.147 22.337 1 43.58 ? C4' C2E 350 A 1 HETATM 7 O O4' C2E . . . C 2 -0.429 -21.738 21.59 1 41.13 ? O4' C2E 350 A 1 HETATM 8 C C3' C2E . . . C 2 0.008 -23.355 23.12 1 41.29 ? C3' C2E 350 A 1 HETATM 9 O O3' C2E . . . C 2 0.55 -23.26 24.354 1 47.51 ? O3' C2E 350 A 1 HETATM 10 C C2' C2E . . . C 2 -1.506 -23.107 23.205 1 42.09 ? C2' C2E 350 A 1 HETATM 11 O O2' C2E . . . C 2 -1.715 -22.144 24.348 1 42.42 ? O2' C2E 350 A 1 HETATM 12 C C1' C2E . . . C 2 -1.773 -22.365 22.189 1 42.63 ? C1' C2E 350 A 1 HETATM 13 N N9 C2E . . . C 2 -2.526 -22.788 21.023 1 42.75 ? N9 C2E 350 A 1 HETATM 14 C C8 C2E . . . C 2 -2.108 -24.052 20.711 1 39.65 ? C8 C2E 350 A 1 HETATM 15 N N7 C2E . . . C 2 -2.811 -24.442 19.574 1 40.96 ? N7 C2E 350 A 1 HETATM 16 C C5 C2E . . . C 2 -3.611 -23.396 19.223 1 39.46 ? C5 C2E 350 A 1 HETATM 17 C C6 C2E . . . C 2 -4.621 -23.061 18.129 1 40.46 ? C6 C2E 350 A 1 HETATM 18 O O6 C2E . . . C 2 -4.888 -23.83 17.269 1 43.12 ? O6 C2E 350 A 1 HETATM 19 N N1 C2E . . . C 2 -5.238 -21.777 18.121 1 36.87 ? N1 C2E 350 A 1 HETATM 20 C C2 C2E . . . C 2 -4.948 -20.79 19.136 1 38.05 ? C2 C2E 350 A 1 HETATM 21 N N2 C2E . . . C 2 -5.541 -19.506 19.152 1 40.48 ? N2 C2E 350 A 1 HETATM 22 N N3 C2E . . . C 2 -4.006 -21.093 20.157 1 35.08 ? N3 C2E 350 A 1 HETATM 23 C C4 C2E . . . C 2 -3.379 -22.411 20.131 1 36.22 ? C4 C2E 350 A 1 HETATM 24 P P11 C2E . . . C 2 0.715 -24.777 25.128 1 45.25 ? P11 C2E 350 A 1 HETATM 25 O O21 C2E . . . C 2 -0.594 -25.53 25.321 1 47.64 ? O21 C2E 350 A 1 HETATM 26 O O11 C2E . . . C 2 1.318 -24.526 26.475 1 47.62 -1 O11 C2E 350 A 1 HETATM 27 O O5A C2E . . . C 2 1.769 -25.631 24.04 1 46.57 ? O5A C2E 350 A 1 HETATM 28 C C5A C2E . . . C 2 3.165 -25.488 24.234 1 44.85 ? C5A C2E 350 A 1 HETATM 29 C C4A C2E . . . C 2 3.767 -26.427 23.218 1 48.55 ? C4A C2E 350 A 1 HETATM 30 O O4A C2E . . . C 2 3.876 -27.658 23.656 1 53.19 ? O4A C2E 350 A 1 HETATM 31 C C3A C2E . . . C 2 2.795 -26.48 21.857 1 46.55 ? C3A C2E 350 A 1 HETATM 32 O O3A C2E . . . C 2 3.351 -25.387 20.937 1 45.54 ? O3A C2E 350 A 1 HETATM 33 C C2A C2E . . . C 2 2.946 -27.617 21.38 1 49.37 ? C2A C2E 350 A 1 HETATM 34 O O2A C2E . . . C 2 4.185 -27.675 20.509 1 48.52 ? O2A C2E 350 A 1 HETATM 35 C C1A C2E . . . C 2 3.238 -28.585 22.645 1 51.93 ? C1A C2E 350 A 1 HETATM 36 N N91 C2E . . . C 2 2.158 -29.15 23.191 1 54.24 ? N91 C2E 350 A 1 HETATM 37 C C81 C2E . . . C 2 0.856 -28.75 23.37 1 53.82 ? C81 C2E 350 A 1 HETATM 38 N N71 C2E . . . C 2 0.2 -29.753 24.034 1 47.03 ? N71 C2E 350 A 1 HETATM 39 C C51 C2E . . . C 2 1.096 -30.743 24.251 1 46.92 ? C51 C2E 350 A 1 HETATM 40 C C61 C2E . . . C 2 0.985 -32.107 24.946 1 51.49 ? C61 C2E 350 A 1 HETATM 41 O O61 C2E . . . C 2 -0.017 -32.475 25.407 1 57.8 ? O61 C2E 350 A 1 HETATM 42 N N11 C2E . . . C 2 2.134 -32.968 25.037 1 60.9 ? N11 C2E 350 A 1 HETATM 43 C C21 C2E . . . C 2 3.401 -32.549 24.492 1 61.31 ? C21 C2E 350 A 1 HETATM 44 N N21 C2E . . . C 2 4.588 -33.449 24.599 1 63.29 ? N21 C2E 350 A 1 HETATM 45 N N31 C2E . . . C 2 3.514 -31.242 23.823 1 57.21 ? N31 C2E 350 A 1 HETATM 46 C C41 C2E . . . C 2 2.313 -30.355 23.733 1 50.28 ? C41 C2E 350 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 430 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #