data_4F5D # _model_server_result.job_id 1bre3nLHkofvr0LBWLl1RQ _model_server_result.datetime_utc '2024-12-26 19:17:02' _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 4f5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4F5D # _exptl.entry_id 4F5D _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 1 _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 4F5D _cell.length_a 111.85 _cell.length_b 111.85 _cell.length_c 35.02 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4F5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A O GLY 43 A GLY 166 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? metalc ? metalc2 A OH TYR 117 A TYR 240 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc3 C O2P C2E . A C2E 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc4 C O21 C2E . A C2E 401 1_555 E MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? # _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 4F5D _atom_sites.fract_transf_matrix[1][1] 0.008941 _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] 0.008941 _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] 0.028555 _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 1 401 401 C2E C2E . D 3 MG A 1 402 2 MG MG . E 3 MG B 1 401 1 MG MG . F 4 HOH A 1 501 2 HOH HOH . G 4 HOH B 1 501 1 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 33.343 -20.873 0.895 1 52.18 ? P1 C2E 401 A 1 HETATM 2 O O2P C2E . . . C 2 33.965 -19.661 0.489 1 23.02 ? O2P C2E 401 A 1 HETATM 3 O O1P C2E . . . C 2 32.502 -21.314 -0.174 1 64.93 ? O1P C2E 401 A 1 HETATM 4 O O5' C2E . . . C 2 34.538 -21.743 0.994 1 18.77 ? O5' C2E 401 A 1 HETATM 5 C C5' C2E . . . C 2 34.309 -22.972 1.442 1 30.04 ? C5' C2E 401 A 1 HETATM 6 C C4' C2E . . . C 2 35.589 -23.573 1.828 1 22.43 ? C4' C2E 401 A 1 HETATM 7 O O4' C2E . . . C 2 36.473 -23.08 0.95 1 26.3 ? O4' C2E 401 A 1 HETATM 8 C C3' C2E . . . C 2 36.088 -22.948 3.035 1 26.99 ? C3' C2E 401 A 1 HETATM 9 O O3' C2E . . . C 2 35.549 -23.491 4.164 1 39.03 ? O3' C2E 401 A 1 HETATM 10 C C2' C2E . . . C 2 37.349 -23.459 2.948 1 35.21 ? C2' C2E 401 A 1 HETATM 11 O O2' C2E . . . C 2 37.228 -24.767 3.211 1 42.1 ? O2' C2E 401 A 1 HETATM 12 C C1' C2E . . . C 2 37.671 -23.319 1.547 1 29.43 ? C1' C2E 401 A 1 HETATM 13 N N9 C2E . . . C 2 38.354 -22.13 1.474 1 32.99 ? N9 C2E 401 A 1 HETATM 14 C C8 C2E . . . C 2 37.795 -21.071 1.137 1 39.41 ? C8 C2E 401 A 1 HETATM 15 N N7 C2E . . . C 2 38.527 -20.125 1.122 1 46.88 ? N7 C2E 401 A 1 HETATM 16 C C5 C2E . . . C 2 39.724 -20.391 1.447 1 43.84 ? C5 C2E 401 A 1 HETATM 17 C C6 C2E . . . C 2 40.873 -19.704 1.577 1 40.36 ? C6 C2E 401 A 1 HETATM 18 O O6 C2E . . . C 2 40.918 -18.405 1.357 1 44.4 ? O6 C2E 401 A 1 HETATM 19 N N1 C2E . . . C 2 41.967 -20.323 1.93 1 42.86 ? N1 C2E 401 A 1 HETATM 20 C C2 C2E . . . C 2 41.92 -21.624 2.17 1 52.63 ? C2 C2E 401 A 1 HETATM 21 N N2 C2E . . . C 2 43.132 -22.194 2.558 1 45.78 ? N2 C2E 401 A 1 HETATM 22 N N3 C2E . . . C 2 40.816 -22.361 2.064 1 54.59 ? N3 C2E 401 A 1 HETATM 23 C C4 C2E . . . C 2 39.685 -21.782 1.712 1 41.93 ? C4 C2E 401 A 1 HETATM 24 P P11 C2E . . . C 2 35.11 -22.576 5.268 1 33.16 ? P11 C2E 401 A 1 HETATM 25 O O21 C2E . . . C 2 36.297 -21.879 5.579 1 14.35 ? O21 C2E 401 A 1 HETATM 26 O O11 C2E . . . C 2 34.755 -23.391 6.375 1 21.77 ? O11 C2E 401 A 1 HETATM 27 O O5A C2E . . . C 2 34.18 -21.434 5.187 1 36.61 ? O5A C2E 401 A 1 HETATM 28 C C5A C2E . . . C 2 32.956 -21.706 4.738 1 22.15 ? C5A C2E 401 A 1 HETATM 29 C C4A C2E . . . C 2 32.316 -20.458 4.349 1 27.58 ? C4A C2E 401 A 1 HETATM 30 O O4A C2E . . . C 2 32.851 -19.554 5.276 1 29.89 ? O4A C2E 401 A 1 HETATM 31 C C3A C2E . . . C 2 32.934 -19.951 3.166 1 41.21 ? C3A C2E 401 A 1 HETATM 32 O O3A C2E . . . C 2 32.402 -20.462 2.014 1 60.37 ? O3A C2E 401 A 1 HETATM 33 C C2A C2E . . . C 2 32.502 -18.597 3.285 1 47.42 ? C2A C2E 401 A 1 HETATM 34 O O2A C2E . . . C 2 31.209 -18.588 2.993 1 53.21 ? O2A C2E 401 A 1 HETATM 35 C C1A C2E . . . C 2 32.641 -18.326 4.704 1 35.42 ? C1A C2E 401 A 1 HETATM 36 N N91 C2E . . . C 2 33.818 -17.612 4.777 1 26.52 ? N91 C2E 401 A 1 HETATM 37 C C81 C2E . . . C 2 34.878 -18.152 5.121 1 32.72 ? C81 C2E 401 A 1 HETATM 38 N N71 C2E . . . C 2 35.816 -17.408 5.142 1 46.81 ? N71 C2E 401 A 1 HETATM 39 C C51 C2E . . . C 2 35.542 -16.218 4.819 1 37.29 ? C51 C2E 401 A 1 HETATM 40 C C61 C2E . . . C 2 36.183 -15.048 4.677 1 32.09 ? C61 C2E 401 A 1 HETATM 41 O O61 C2E . . . C 2 37.496 -14.973 4.903 1 45.49 ? O61 C2E 401 A 1 HETATM 42 N N11 C2E . . . C 2 35.564 -13.964 4.325 1 37.76 ? N11 C2E 401 A 1 HETATM 43 C C21 C2E . . . C 2 34.268 -14.016 4.084 1 46.7 ? C21 C2E 401 A 1 HETATM 44 N N21 C2E . . . C 2 33.671 -12.81 3.685 1 32.91 ? N21 C2E 401 A 1 HETATM 45 N N31 C2E . . . C 2 33.58 -15.149 4.193 1 49.5 ? N31 C2E 401 A 1 HETATM 46 C C41 C2E . . . C 2 34.164 -16.273 4.54 1 33.67 ? C41 C2E 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #