data_5Y6G # _model_server_result.job_id ZNtHRZFaz5iu7sT-7zSe7A _model_server_result.datetime_utc '2025-02-05 07:49:34' _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 5y6g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5Y6G # _exptl.entry_id 5Y6G _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 5Y6G _cell.length_a 110.34 _cell.length_b 110.34 _cell.length_c 35.57 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y6G _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 B N N ? 2 C 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 5Y6G _atom_sites.fract_transf_matrix[1][1] 0.009063 _atom_sites.fract_transf_matrix[1][2] 0.005232 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010465 _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] 0.028113 _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 C2E A 1 301 1 C2E C2E . C 2 C2E A 1 302 2 C2E C2E . D 3 SO4 A 1 303 1 SO4 SO4 . E 4 HOH A 1 401 19 HOH HOH . E 4 HOH A 2 402 45 HOH HOH . E 4 HOH A 3 403 1 HOH HOH . E 4 HOH A 4 404 9 HOH HOH . E 4 HOH A 5 405 13 HOH HOH . E 4 HOH A 6 406 23 HOH HOH . E 4 HOH A 7 407 21 HOH HOH . E 4 HOH A 8 408 5 HOH HOH . E 4 HOH A 9 409 4 HOH HOH . E 4 HOH A 10 410 43 HOH HOH . E 4 HOH A 11 411 17 HOH HOH . E 4 HOH A 12 412 16 HOH HOH . E 4 HOH A 13 413 30 HOH HOH . E 4 HOH A 14 414 8 HOH HOH . E 4 HOH A 15 415 36 HOH HOH . E 4 HOH A 16 416 2 HOH HOH . E 4 HOH A 17 417 24 HOH HOH . E 4 HOH A 18 418 14 HOH HOH . E 4 HOH A 19 419 28 HOH HOH . E 4 HOH A 20 420 27 HOH HOH . E 4 HOH A 21 421 32 HOH HOH . E 4 HOH A 22 422 3 HOH HOH . E 4 HOH A 23 423 29 HOH HOH . E 4 HOH A 24 424 15 HOH HOH . E 4 HOH A 25 425 6 HOH HOH . E 4 HOH A 26 426 11 HOH HOH . E 4 HOH A 27 427 41 HOH HOH . E 4 HOH A 28 428 25 HOH HOH . E 4 HOH A 29 429 18 HOH HOH . E 4 HOH A 30 430 38 HOH HOH . E 4 HOH A 31 431 7 HOH HOH . E 4 HOH A 32 432 42 HOH HOH . E 4 HOH A 33 433 10 HOH HOH . E 4 HOH A 34 434 12 HOH HOH . E 4 HOH A 35 435 22 HOH HOH . E 4 HOH A 36 436 44 HOH HOH . E 4 HOH A 37 437 40 HOH HOH . E 4 HOH A 38 438 26 HOH HOH . E 4 HOH A 39 439 35 HOH HOH . E 4 HOH A 40 440 37 HOH HOH . E 4 HOH A 41 441 33 HOH HOH . E 4 HOH A 42 442 34 HOH HOH . E 4 HOH A 43 443 31 HOH HOH . E 4 HOH A 44 444 20 HOH HOH . E 4 HOH A 45 445 39 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 -35.415 40.603 -6.136 1 40.01 ? P1 C2E 302 A 1 HETATM 2 O O2P C2E . . . C 2 -35.62 41.72 -7.272 1 33.52 ? O2P C2E 302 A 1 HETATM 3 O O1P C2E . . . C 2 -36.463 40.763 -5.104 1 66.72 ? O1P C2E 302 A 1 HETATM 4 O O5' C2E . . . C 2 -35.511 39.134 -6.785 1 33.14 ? O5' C2E 302 A 1 HETATM 5 C C5' C2E . . . C 2 -35.566 37.954 -5.985 1 39.05 ? C5' C2E 302 A 1 HETATM 6 C C4' C2E . . . C 2 -35.292 36.708 -6.83 1 51.59 ? C4' C2E 302 A 1 HETATM 7 O O4' C2E . . . C 2 -36.162 36.664 -7.966 1 49.85 ? O4' C2E 302 A 1 HETATM 8 C C3' C2E . . . C 2 -33.873 36.72 -7.414 1 44.92 ? C3' C2E 302 A 1 HETATM 9 O O3' C2E . . . C 2 -32.891 36.234 -6.498 1 57.98 ? O3' C2E 302 A 1 HETATM 10 C C2' C2E . . . C 2 -34.033 35.759 -8.601 1 30.77 ? C2' C2E 302 A 1 HETATM 11 O O2' C2E . . . C 2 -33.834 34.409 -8.182 1 36.35 ? O2' C2E 302 A 1 HETATM 12 C C1' C2E . . . C 2 -35.491 35.987 -9.035 1 40.2 ? C1' C2E 302 A 1 HETATM 13 N N9 C2E . . . C 2 -35.5 36.803 -10.252 1 33.38 ? N9 C2E 302 A 1 HETATM 14 C C8 C2E . . . C 2 -35.956 38.083 -10.379 1 34.77 ? C8 C2E 302 A 1 HETATM 15 N N7 C2E . . . C 2 -35.799 38.484 -11.607 1 35.82 ? N7 C2E 302 A 1 HETATM 16 C C5 C2E . . . C 2 -35.234 37.491 -12.338 1 28.21 ? C5 C2E 302 A 1 HETATM 17 C C6 C2E . . . C 2 -34.843 37.358 -13.693 1 21.45 ? C6 C2E 302 A 1 HETATM 18 O O6 C2E . . . C 2 -34.995 38.273 -14.487 1 29.06 ? O6 C2E 302 A 1 HETATM 19 N N1 C2E . . . C 2 -34.294 36.189 -14.087 1 21.47 ? N1 C2E 302 A 1 HETATM 20 C C2 C2E . . . C 2 -34.128 35.17 -13.197 1 26.81 ? C2 C2E 302 A 1 HETATM 21 N N2 C2E . . . C 2 -33.567 33.997 -13.631 1 25.35 ? N2 C2E 302 A 1 HETATM 22 N N3 C2E . . . C 2 -34.486 35.279 -11.938 1 34.42 ? N3 C2E 302 A 1 HETATM 23 C C4 C2E . . . C 2 -35.036 36.408 -11.475 1 25.47 ? C4 C2E 302 A 1 HETATM 24 P P11 C2E . . . C 2 -31.324 36.562 -6.677 1 45.27 ? P11 C2E 302 A 1 HETATM 25 O O21 C2E . . . C 2 -30.849 36.133 -8.157 1 46.7 ? O21 C2E 302 A 1 HETATM 26 O O11 C2E . . . C 2 -30.539 35.81 -5.674 1 48.69 ? O11 C2E 302 A 1 HETATM 27 O O5A C2E . . . C 2 -31.101 38.143 -6.463 1 37.73 ? O5A C2E 302 A 1 HETATM 28 C C5A C2E . . . C 2 -31.404 38.779 -5.221 1 44.38 ? C5A C2E 302 A 1 HETATM 29 C C4A C2E . . . C 2 -31.541 40.296 -5.377 1 41.99 ? C4A C2E 302 A 1 HETATM 30 O O4A C2E . . . C 2 -30.395 40.843 -6.036 1 43.54 ? O4A C2E 302 A 1 HETATM 31 C C3A C2E . . . C 2 -32.748 40.664 -6.248 1 49.89 ? C3A C2E 302 A 1 HETATM 32 O O3A C2E . . . C 2 -33.952 40.784 -5.485 1 56.85 ? O3A C2E 302 A 1 HETATM 33 C C2A C2E . . . C 2 -32.325 42.038 -6.789 1 52.27 ? C2A C2E 302 A 1 HETATM 34 O O2A C2E . . . C 2 -32.716 43.061 -5.869 1 58.72 ? O2A C2E 302 A 1 HETATM 35 C C1A C2E . . . C 2 -30.796 41.924 -6.885 1 46.93 ? C1A C2E 302 A 1 HETATM 36 N N91 C2E . . . C 2 -30.414 41.642 -8.273 1 36.7 ? N91 C2E 302 A 1 HETATM 37 C C81 C2E . . . C 2 -29.897 40.471 -8.749 1 25.97 ? C81 C2E 302 A 1 HETATM 38 N N71 C2E . . . C 2 -29.678 40.572 -10.027 1 36.74 ? N71 C2E 302 A 1 HETATM 39 C C51 C2E . . . C 2 -30.041 41.806 -10.454 1 22.46 ? C51 C2E 302 A 1 HETATM 40 C C61 C2E . . . C 2 -30.026 42.463 -11.71 1 33.99 ? C61 C2E 302 A 1 HETATM 41 O O61 C2E . . . C 2 -29.621 41.899 -12.715 1 37.23 ? O61 C2E 302 A 1 HETATM 42 N N11 C2E . . . C 2 -30.476 43.735 -11.768 1 32.74 ? N11 C2E 302 A 1 HETATM 43 C C21 C2E . . . C 2 -30.928 44.357 -10.642 1 37.33 ? C21 C2E 302 A 1 HETATM 44 N N21 C2E . . . C 2 -31.377 45.648 -10.736 1 43.7 ? N21 C2E 302 A 1 HETATM 45 N N31 C2E . . . C 2 -30.946 43.76 -9.474 1 30.29 ? N31 C2E 302 A 1 HETATM 46 C C41 C2E . . . C 2 -30.516 42.502 -9.335 1 26.67 ? C41 C2E 302 A 1 HETATM 47 H "H5'1" C2E . . . C 2 -36.448 37.88 -5.586 1 46.87 ? "H5'1" C2E 302 A 1 HETATM 48 H "H5'2" C2E . . . C 2 -34.902 38.014 -5.28 1 46.87 ? "H5'2" C2E 302 A 1 HETATM 49 H H4' C2E . . . C 2 -35.417 35.911 -6.291 1 61.92 ? H4' C2E 302 A 1 HETATM 50 H H3' C2E . . . C 2 -33.636 37.607 -7.727 1 53.91 ? H3' C2E 302 A 1 HETATM 51 H H2' C2E . . . C 2 -33.42 35.991 -9.316 1 36.93 ? H2' C2E 302 A 1 HETATM 52 H HO2' C2E . . . C 2 -33.587 33.887 -8.806 1 43.63 ? HO2' C2E 302 A 1 HETATM 53 H H1' C2E . . . C 2 -35.921 35.135 -9.208 1 48.25 ? H1' C2E 302 A 1 HETATM 54 H H8 C2E . . . C 2 -36.325 38.591 -9.693 1 41.73 ? H8 C2E 302 A 1 HETATM 55 H HN1 C2E . . . C 2 -34.048 36.086 -14.904 1 25.77 ? HN1 C2E 302 A 1 HETATM 56 H HN21 C2E . . . C 2 -33.328 33.913 -14.453 1 30.43 ? HN21 C2E 302 A 1 HETATM 57 H HN22 C2E . . . C 2 -33.455 33.344 -13.082 1 30.43 ? HN22 C2E 302 A 1 HETATM 58 H H511 C2E . . . C 2 -32.238 38.421 -4.877 1 53.26 ? H511 C2E 302 A 1 HETATM 59 H H512 C2E . . . C 2 -30.695 38.59 -4.587 1 53.26 ? H512 C2E 302 A 1 HETATM 60 H H4A C2E . . . C 2 -31.637 40.705 -4.503 1 50.39 ? H4A C2E 302 A 1 HETATM 61 H H3A C2E . . . C 2 -32.86 40.032 -6.975 1 59.88 ? H3A C2E 302 A 1 HETATM 62 H H2A C2E . . . C 2 -32.713 42.197 -7.663 1 62.73 ? H2A C2E 302 A 1 HETATM 63 H HO2A C2E . . . C 2 -32.633 43.85 -6.173 1 70.47 ? HO2A C2E 302 A 1 HETATM 64 H H1A C2E . . . C 2 -30.382 42.75 -6.589 1 56.33 ? H1A C2E 302 A 1 HETATM 65 H H81 C2E . . . C 2 -29.725 39.715 -8.235 1 31.17 ? H81 C2E 302 A 1 HETATM 66 H HN11 C2E . . . C 2 -30.479 44.154 -12.519 1 39.29 ? HN11 C2E 302 A 1 HETATM 67 H HN24 C2E . . . C 2 -31.665 46.056 -10.035 1 52.45 ? HN24 C2E 302 A 1 HETATM 68 H HN23 C2E . . . C 2 -31.372 46.051 -11.495 1 52.45 ? HN23 C2E 302 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 68 #