data_4F9G # _model_server_result.job_id T8ePpinAfI68BiBxyjbRqg _model_server_result.datetime_utc '2024-10-13 00:26:09' _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 4f9g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4F9G # _exptl.entry_id 4F9G _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 96.32 _cell.angle_gamma 90 _cell.entry_id 4F9G _cell.length_a 60.027 _cell.length_b 74.2 _cell.length_c 60.013 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4F9G _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 # _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 4F9G _atom_sites.fract_transf_matrix[1][1] 0.016659 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001844 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013477 _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] 0.016765 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id C2E _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 401 _pdbx_nonpoly_scheme.auth_seq_num 401 _pdbx_nonpoly_scheme.pdb_mon_id C2E _pdbx_nonpoly_scheme.auth_mon_id C2E _pdbx_nonpoly_scheme.pdb_ins_code . # 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 12.835 7.719 12.588 1 100.69 ? P1 C2E 401 A 1 HETATM 2 O O2P C2E . . . C 2 11.772 6.618 12.812 1 92.17 ? O2P C2E 401 A 1 HETATM 3 O O1P C2E . . . C 2 13.51 7.472 11.179 1 96.46 ? O1P C2E 401 A 1 HETATM 4 O O5' C2E . . . C 2 13.9 7.567 13.782 1 83.18 ? O5' C2E 401 A 1 HETATM 5 C C5' C2E . . . C 2 13.628 7.715 15.091 1 76.26 ? C5' C2E 401 A 1 HETATM 6 C C4' C2E . . . C 2 14.833 7.618 15.923 1 87.28 ? C4' C2E 401 A 1 HETATM 7 O O4' C2E . . . C 2 15.64 6.612 15.43 1 90.42 ? O4' C2E 401 A 1 HETATM 8 C C3' C2E . . . C 2 15.709 8.764 15.761 1 89.71 ? C3' C2E 401 A 1 HETATM 9 O O3' C2E . . . C 2 15.258 9.909 16.424 1 97.03 ? O3' C2E 401 A 1 HETATM 10 C C2' C2E . . . C 2 16.93 8.295 16.274 1 89.55 ? C2' C2E 401 A 1 HETATM 11 O O2' C2E . . . C 2 16.905 8.33 17.677 1 92.02 ? O2' C2E 401 A 1 HETATM 12 C C1' C2E . . . C 2 16.965 6.9 15.796 1 82.07 ? C1' C2E 401 A 1 HETATM 13 N N9 C2E . . . C 2 17.786 6.649 14.613 1 82.54 ? N9 C2E 401 A 1 HETATM 14 C C8 C2E . . . C 2 17.294 6.715 13.372 1 83.21 ? C8 C2E 401 A 1 HETATM 15 N N7 C2E . . . C 2 18.259 6.425 12.485 1 74.01 ? N7 C2E 401 A 1 HETATM 16 C C5 C2E . . . C 2 19.398 6.173 13.142 1 86.81 ? C5 C2E 401 A 1 HETATM 17 C C6 C2E . . . C 2 20.692 5.818 12.713 1 95.35 ? C6 C2E 401 A 1 HETATM 18 O O6 C2E . . . C 2 20.973 5.695 11.396 1 87.2 ? O6 C2E 401 A 1 HETATM 19 N N1 C2E . . . C 2 21.621 5.606 13.671 1 93.36 ? N1 C2E 401 A 1 HETATM 20 C C2 C2E . . . C 2 21.338 5.723 14.989 1 91.13 ? C2 C2E 401 A 1 HETATM 21 N N2 C2E . . . C 2 22.385 5.473 15.924 1 91.47 ? N2 C2E 401 A 1 HETATM 22 N N3 C2E . . . C 2 20.104 6.067 15.42 1 85.14 ? N3 C2E 401 A 1 HETATM 23 C C4 C2E . . . C 2 19.107 6.304 14.516 1 87.46 ? C4 C2E 401 A 1 HETATM 24 P P11 C2E . . . C 2 15.459 11.285 15.7 1 101.35 ? P11 C2E 401 A 1 HETATM 25 O O21 C2E . . . C 2 15.665 12.247 16.772 1 85.07 ? O21 C2E 401 A 1 HETATM 26 O O11 C2E . . . C 2 16.753 11.252 14.774 1 82.53 ? O11 C2E 401 A 1 HETATM 27 O O5A C2E . . . C 2 14.166 11.845 14.898 1 81.76 ? O5A C2E 401 A 1 HETATM 28 C C5A C2E . . . C 2 13.031 11.132 14.509 1 72.5 ? C5A C2E 401 A 1 HETATM 29 C C4A C2E . . . C 2 12.546 11.347 13.151 1 83.35 ? C4A C2E 401 A 1 HETATM 30 O O4A C2E . . . C 2 13.268 12.378 12.498 1 89.01 ? O4A C2E 401 A 1 HETATM 31 C C3A C2E . . . C 2 12.847 10.261 12.253 1 91.38 ? C3A C2E 401 A 1 HETATM 32 O O3A C2E . . . C 2 12.074 9.084 12.545 1 89.01 ? O3A C2E 401 A 1 HETATM 33 C C2A C2E . . . C 2 12.455 10.834 11.028 1 91.7 ? C2A C2E 401 A 1 HETATM 34 O O2A C2E . . . C 2 11.074 10.873 11.011 1 92.52 ? O2A C2E 401 A 1 HETATM 35 C C1A C2E . . . C 2 13.013 12.226 11.143 1 86.05 ? C1A C2E 401 A 1 HETATM 36 N N91 C2E . . . C 2 14.276 12.497 10.446 1 82.42 ? N91 C2E 401 A 1 HETATM 37 C C81 C2E . . . C 2 15.465 12.483 11.08 1 79.49 ? C81 C2E 401 A 1 HETATM 38 N N71 C2E . . . C 2 16.459 12.779 10.22 1 82.62 ? N71 C2E 401 A 1 HETATM 39 C C51 C2E . . . C 2 15.909 12.99 8.994 1 97.76 ? C51 C2E 401 A 1 HETATM 40 C C61 C2E . . . C 2 16.466 13.33 7.752 1 100.32 ? C61 C2E 401 A 1 HETATM 41 O O61 C2E . . . C 2 17.753 13.497 7.597 1 93.47 ? O61 C2E 401 A 1 HETATM 42 N N11 C2E . . . C 2 15.641 13.484 6.715 1 98.22 ? N11 C2E 401 A 1 HETATM 43 C C21 C2E . . . C 2 14.306 13.329 6.866 1 95.87 ? C21 C2E 401 A 1 HETATM 44 N N21 C2E . . . C 2 13.502 13.532 5.71 1 93.59 ? N21 C2E 401 A 1 HETATM 45 N N31 C2E . . . C 2 13.744 13.004 8.049 1 85.85 ? N31 C2E 401 A 1 HETATM 46 C C41 C2E . . . C 2 14.509 12.82 9.134 1 86.22 ? C41 C2E 401 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 46 #