data_5Y6G # _model_server_result.job_id fYenno9i3CAfg9JXT3h9gQ _model_server_result.datetime_utc '2025-02-05 07:55:14' _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":"B","auth_seq_id":301}' # _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 . . . B 2 -29.599 40.911 -17.299 1 37.34 ? P1 C2E 301 A 1 HETATM 2 O O2P C2E . . . B 2 -29.231 39.702 -16.312 1 30.19 ? O2P C2E 301 A 1 HETATM 3 O O1P C2E . . . B 2 -29.928 40.38 -18.645 1 43.01 ? O1P C2E 301 A 1 HETATM 4 O O5' C2E . . . B 2 -30.84 41.747 -16.715 1 31.45 ? O5' C2E 301 A 1 HETATM 5 C C5' C2E . . . B 2 -31.421 42.833 -17.429 1 34.01 ? C5' C2E 301 A 1 HETATM 6 C C4' C2E . . . B 2 -32.362 43.638 -16.529 1 45.78 ? C4' C2E 301 A 1 HETATM 7 O O4' C2E . . . B 2 -33.374 42.797 -15.964 1 44.7 ? O4' C2E 301 A 1 HETATM 8 C C3' C2E . . . B 2 -31.623 44.235 -15.323 1 45.6 ? C3' C2E 301 A 1 HETATM 9 O O3' C2E . . . B 2 -30.941 45.447 -15.649 1 50.72 ? O3' C2E 301 A 1 HETATM 10 C C2' C2E . . . B 2 -32.796 44.485 -14.364 1 44.94 ? C2' C2E 301 A 1 HETATM 11 O O2' C2E . . . B 2 -33.485 45.696 -14.679 1 43.53 ? O2' C2E 301 A 1 HETATM 12 C C1' C2E . . . B 2 -33.691 43.272 -14.646 1 42.76 ? C1' C2E 301 A 1 HETATM 13 N N9 C2E . . . B 2 -33.404 42.248 -13.642 1 25.29 ? N9 C2E 301 A 1 HETATM 14 C C8 C2E . . . B 2 -32.662 41.117 -13.821 1 23.56 ? C8 C2E 301 A 1 HETATM 15 N N7 C2E . . . B 2 -32.624 40.443 -12.711 1 27.26 ? N7 C2E 301 A 1 HETATM 16 C C5 C2E . . . B 2 -33.334 41.095 -11.759 1 28.12 ? C5 C2E 301 A 1 HETATM 17 C C6 C2E . . . B 2 -33.624 40.834 -10.401 1 28.55 ? C6 C2E 301 A 1 HETATM 18 O O6 C2E . . . B 2 -33.198 39.83 -9.851 1 24.15 ? O6 C2E 301 A 1 HETATM 19 N N1 C2E . . . B 2 -34.385 41.726 -9.73 1 29.28 ? N1 C2E 301 A 1 HETATM 20 C C2 C2E . . . B 2 -34.854 42.844 -10.355 1 34.93 ? C2 C2E 301 A 1 HETATM 21 N N2 C2E . . . B 2 -35.625 43.73 -9.644 1 41.35 ? N2 C2E 301 A 1 HETATM 22 N N3 C2E . . . B 2 -34.588 43.098 -11.618 1 38.08 ? N3 C2E 301 A 1 HETATM 23 C C4 C2E . . . B 2 -33.84 42.258 -12.345 1 31.19 ? C4 C2E 301 A 1 HETATM 24 P P11 C2E . . . B 2 -29.666 45.957 -14.812 1 41.88 ? P11 C2E 301 A 1 HETATM 25 O O21 C2E . . . B 2 -30.003 45.881 -13.24 1 40.82 ? O21 C2E 301 A 1 HETATM 26 O O11 C2E . . . B 2 -29.362 47.352 -15.202 1 44.2 ? O11 C2E 301 A 1 HETATM 27 O O5A C2E . . . B 2 -28.403 45.01 -15.127 1 41.48 ? O5A C2E 301 A 1 HETATM 28 C C5A C2E . . . B 2 -27.836 44.937 -16.431 1 40.6 ? C5A C2E 301 A 1 HETATM 29 C C4A C2E . . . B 2 -26.933 43.709 -16.556 1 40.71 ? C4A C2E 301 A 1 HETATM 30 O O4A C2E . . . B 2 -25.883 43.757 -15.587 1 36.8 ? O4A C2E 301 A 1 HETATM 31 C C3A C2E . . . B 2 -27.682 42.406 -16.262 1 46.55 ? C3A C2E 301 A 1 HETATM 32 O O3A C2E . . . B 2 -28.339 41.905 -17.421 1 48.18 ? O3A C2E 301 A 1 HETATM 33 C C2A C2E . . . B 2 -26.533 41.473 -15.863 1 40.84 ? C2A C2E 301 A 1 HETATM 34 O O2A C2E . . . B 2 -25.885 40.944 -17.024 1 49.37 ? O2A C2E 301 A 1 HETATM 35 C C1A C2E . . . B 2 -25.61 42.434 -15.109 1 34.55 ? C1A C2E 301 A 1 HETATM 36 N N91 C2E . . . B 2 -25.903 42.352 -13.678 1 28.91 ? N91 C2E 301 A 1 HETATM 37 C C81 C2E . . . B 2 -26.608 43.269 -12.954 1 27.1 ? C81 C2E 301 A 1 HETATM 38 N N71 C2E . . . B 2 -26.683 42.883 -11.716 1 29.36 ? N71 C2E 301 A 1 HETATM 39 C C51 C2E . . . B 2 -26.04 41.7 -11.571 1 17.86 ? C51 C2E 301 A 1 HETATM 40 C C61 C2E . . . B 2 -25.806 40.838 -10.475 1 26.52 ? C61 C2E 301 A 1 HETATM 41 O O61 C2E . . . B 2 -26.226 41.108 -9.361 1 41.99 ? O61 C2E 301 A 1 HETATM 42 N N11 C2E . . . B 2 -25.106 39.705 -10.69 1 27.14 ? N11 C2E 301 A 1 HETATM 43 C C21 C2E . . . B 2 -24.641 39.411 -11.937 1 27.62 ? C21 C2E 301 A 1 HETATM 44 N N21 C2E . . . B 2 -23.931 38.251 -12.117 1 36.33 ? N21 C2E 301 A 1 HETATM 45 N N31 C2E . . . B 2 -24.847 40.204 -12.966 1 30.62 ? N31 C2E 301 A 1 HETATM 46 C C41 C2E . . . B 2 -25.535 41.344 -12.827 1 26.68 ? C41 C2E 301 A 1 HETATM 47 H "H5'1" C2E . . . B 2 -31.922 42.485 -18.184 1 40.82 ? "H5'1" C2E 301 A 1 HETATM 48 H "H5'2" C2E . . . B 2 -30.717 43.415 -17.755 1 40.82 ? "H5'2" C2E 301 A 1 HETATM 49 H H4' C2E . . . B 2 -32.777 44.348 -17.042 1 54.94 ? H4' C2E 301 A 1 HETATM 50 H H3' C2E . . . B 2 -31.007 43.591 -14.942 1 54.72 ? H3' C2E 301 A 1 HETATM 51 H H2' C2E . . . B 2 -32.495 44.487 -13.442 1 53.94 ? H2' C2E 301 A 1 HETATM 52 H HO2' C2E . . . B 2 -33.743 45.746 -15.487 1 52.25 ? HO2' C2E 301 A 1 HETATM 53 H H1' C2E . . . B 2 -34.625 43.529 -14.601 1 51.32 ? H1' C2E 301 A 1 HETATM 54 H H8 C2E . . . B 2 -32.249 40.867 -14.615 1 28.27 ? H8 C2E 301 A 1 HETATM 55 H HN1 C2E . . . B 2 -34.575 41.587 -8.903 1 35.14 ? HN1 C2E 301 A 1 HETATM 56 H HN21 C2E . . . B 2 -35.805 43.576 -8.817 1 49.62 ? HN21 C2E 301 A 1 HETATM 57 H HN22 C2E . . . B 2 -35.927 44.439 -10.024 1 49.62 ? HN22 C2E 301 A 1 HETATM 58 H H511 C2E . . . B 2 -28.548 44.879 -17.087 1 48.73 ? H511 C2E 301 A 1 HETATM 59 H H512 C2E . . . B 2 -27.313 45.736 -16.599 1 48.73 ? H512 C2E 301 A 1 HETATM 60 H H4A C2E . . . B 2 -26.552 43.671 -17.448 1 48.85 ? H4A C2E 301 A 1 HETATM 61 H H3A C2E . . . B 2 -28.304 42.516 -15.526 1 55.86 ? H3A C2E 301 A 1 HETATM 62 H H2A C2E . . . B 2 -26.846 40.762 -15.282 1 49.01 ? H2A C2E 301 A 1 HETATM 63 H HO2A C2E . . . B 2 -25.036 40.944 -16.976 1 59.25 ? HO2A C2E 301 A 1 HETATM 64 H H1A C2E . . . B 2 -24.682 42.204 -15.273 1 41.47 ? H1A C2E 301 A 1 HETATM 65 H H81 C2E . . . B 2 -26.974 44.054 -13.294 1 32.52 ? H81 C2E 301 A 1 HETATM 66 H HN11 C2E . . . B 2 -24.953 39.166 -10.038 1 32.57 ? HN11 C2E 301 A 1 HETATM 67 H HN24 C2E . . . B 2 -23.628 38.048 -12.896 1 43.6 ? HN24 C2E 301 A 1 HETATM 68 H HN23 C2E . . . B 2 -23.79 37.726 -11.451 1 43.6 ? HN23 C2E 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 68 #