data_3PJT # _model_server_result.job_id LTdWDd4w4a6waHtYj4ZIHw _model_server_result.datetime_utc '2025-03-04 16:59:16' _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 3pjt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2256}' # _entry.id 3PJT # _exptl.entry_id 3PJT _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 90 _cell.entry_id 3PJT _cell.length_a 41.445 _cell.length_b 204.83 _cell.length_c 142.391 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PJT _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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 D 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 3PJT _atom_sites.fract_transf_matrix[1][1] 0.024128 _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] 0.004882 _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] 0.007023 _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 2256 2256 C2E C2E . D 2 C2E B 1 2256 2256 C2E C2E . E 3 HOH A 1 1 1 HOH HOH . E 3 HOH A 2 2 2 HOH HOH . E 3 HOH A 3 3 3 HOH HOH . E 3 HOH A 4 4 4 HOH HOH . E 3 HOH A 5 5 5 HOH HOH . E 3 HOH A 6 6 6 HOH HOH . E 3 HOH A 7 7 7 HOH HOH . E 3 HOH A 8 8 8 HOH HOH . E 3 HOH A 9 10 10 HOH HOH . E 3 HOH A 10 11 11 HOH HOH . E 3 HOH A 11 14 14 HOH HOH . E 3 HOH A 12 16 16 HOH HOH . E 3 HOH A 13 17 17 HOH HOH . E 3 HOH A 14 18 18 HOH HOH . E 3 HOH A 15 19 19 HOH HOH . E 3 HOH A 16 20 20 HOH HOH . E 3 HOH A 17 21 21 HOH HOH . E 3 HOH A 18 22 22 HOH HOH . E 3 HOH A 19 23 23 HOH HOH . E 3 HOH A 20 24 24 HOH HOH . E 3 HOH A 21 25 25 HOH HOH . E 3 HOH A 22 26 26 HOH HOH . E 3 HOH A 23 27 27 HOH HOH . E 3 HOH A 24 28 28 HOH HOH . E 3 HOH A 25 30 30 HOH HOH . E 3 HOH A 26 32 32 HOH HOH . E 3 HOH A 27 35 35 HOH HOH . E 3 HOH A 28 36 36 HOH HOH . E 3 HOH A 29 37 37 HOH HOH . E 3 HOH A 30 40 40 HOH HOH . E 3 HOH A 31 44 44 HOH HOH . E 3 HOH A 32 45 45 HOH HOH . E 3 HOH A 33 46 46 HOH HOH . E 3 HOH A 34 47 47 HOH HOH . E 3 HOH A 35 48 48 HOH HOH . E 3 HOH A 36 49 49 HOH HOH . E 3 HOH A 37 50 50 HOH HOH . E 3 HOH A 38 52 52 HOH HOH . E 3 HOH A 39 54 54 HOH HOH . E 3 HOH A 40 56 56 HOH HOH . E 3 HOH A 41 57 57 HOH HOH . E 3 HOH A 42 61 61 HOH HOH . E 3 HOH A 43 62 62 HOH HOH . E 3 HOH A 44 63 63 HOH HOH . E 3 HOH A 45 64 64 HOH HOH . E 3 HOH A 46 65 65 HOH HOH . E 3 HOH A 47 66 66 HOH HOH . E 3 HOH A 48 67 67 HOH HOH . E 3 HOH A 49 69 69 HOH HOH . E 3 HOH A 50 71 71 HOH HOH . E 3 HOH A 51 74 74 HOH HOH . E 3 HOH A 52 75 75 HOH HOH . E 3 HOH A 53 76 76 HOH HOH . E 3 HOH A 54 79 79 HOH HOH . E 3 HOH A 55 80 80 HOH HOH . E 3 HOH A 56 81 81 HOH HOH . E 3 HOH A 57 82 82 HOH HOH . E 3 HOH A 58 83 83 HOH HOH . E 3 HOH A 59 85 85 HOH HOH . E 3 HOH A 60 86 86 HOH HOH . E 3 HOH A 61 87 87 HOH HOH . E 3 HOH A 62 101 101 HOH HOH . E 3 HOH A 63 115 115 HOH HOH . E 3 HOH A 64 649 4 HOH HOH . E 3 HOH A 65 650 6 HOH HOH . E 3 HOH A 66 651 20 HOH HOH . E 3 HOH A 67 652 21 HOH HOH . E 3 HOH A 68 653 27 HOH HOH . E 3 HOH A 69 654 50 HOH HOH . E 3 HOH A 70 655 61 HOH HOH . E 3 HOH A 71 656 66 HOH HOH . E 3 HOH A 72 657 67 HOH HOH . F 3 HOH B 1 9 9 HOH HOH . F 3 HOH B 2 10 10 HOH HOH . F 3 HOH B 3 12 12 HOH HOH . F 3 HOH B 4 13 13 HOH HOH . F 3 HOH B 5 15 15 HOH HOH . F 3 HOH B 6 17 17 HOH HOH . F 3 HOH B 7 22 22 HOH HOH . F 3 HOH B 8 25 25 HOH HOH . F 3 HOH B 9 28 28 HOH HOH . F 3 HOH B 10 29 29 HOH HOH . F 3 HOH B 11 31 31 HOH HOH . F 3 HOH B 12 32 32 HOH HOH . F 3 HOH B 13 33 33 HOH HOH . F 3 HOH B 14 34 34 HOH HOH . F 3 HOH B 15 38 38 HOH HOH . F 3 HOH B 16 39 39 HOH HOH . F 3 HOH B 17 41 41 HOH HOH . F 3 HOH B 18 42 42 HOH HOH . F 3 HOH B 19 43 43 HOH HOH . F 3 HOH B 20 51 51 HOH HOH . F 3 HOH B 21 52 52 HOH HOH . F 3 HOH B 22 53 53 HOH HOH . F 3 HOH B 23 55 55 HOH HOH . F 3 HOH B 24 56 56 HOH HOH . F 3 HOH B 25 58 58 HOH HOH . F 3 HOH B 26 59 59 HOH HOH . F 3 HOH B 27 60 60 HOH HOH . F 3 HOH B 28 63 63 HOH HOH . F 3 HOH B 29 68 68 HOH HOH . F 3 HOH B 30 70 70 HOH HOH . F 3 HOH B 31 72 72 HOH HOH . F 3 HOH B 32 73 73 HOH HOH . F 3 HOH B 33 77 77 HOH HOH . F 3 HOH B 34 78 78 HOH HOH . F 3 HOH B 35 84 84 HOH HOH . F 3 HOH B 36 105 105 HOH HOH . F 3 HOH B 37 117 117 HOH HOH . F 3 HOH B 38 118 118 HOH HOH . F 3 HOH B 39 121 121 HOH HOH . F 3 HOH B 40 649 13 HOH HOH . F 3 HOH B 41 650 15 HOH HOH . F 3 HOH B 42 651 31 HOH HOH . F 3 HOH B 43 652 68 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 . . . D 2 -2.965 -83.127 9.927 1 30.99 ? P1 C2E 2256 B 1 HETATM 2 O O2P C2E . . . D 2 -4.061 -84.166 9.869 1 24.24 ? O2P C2E 2256 B 1 HETATM 3 O O1P C2E . . . D 2 -3.136 -82.272 11.192 1 27.39 ? O1P C2E 2256 B 1 HETATM 4 O O5' C2E . . . D 2 -1.581 -83.874 9.995 1 31.43 ? O5' C2E 2256 B 1 HETATM 5 C C5' C2E . . . D 2 -0.5 -83.09 10.375 1 30.62 ? C5' C2E 2256 B 1 HETATM 6 C C4' C2E . . . D 2 0.317 -82.542 9.243 1 33.71 ? C4' C2E 2256 B 1 HETATM 7 O O4' C2E . . . D 2 1.371 -81.76 9.753 1 32.71 ? O4' C2E 2256 B 1 HETATM 8 C C3' C2E . . . D 2 0.987 -83.647 8.475 1 32.66 ? C3' C2E 2256 B 1 HETATM 9 O O3' C2E . . . D 2 1.5 -83.212 7.266 1 36.43 ? O3' C2E 2256 B 1 HETATM 10 C C2' C2E . . . D 2 2.097 -83.902 9.285 1 32.68 ? C2' C2E 2256 B 1 HETATM 11 O O2' C2E . . . D 2 3.183 -84.324 8.466 1 33.82 ? O2' C2E 2256 B 1 HETATM 12 C C1' C2E . . . D 2 2.434 -82.64 9.931 1 32.2 ? C1' C2E 2256 B 1 HETATM 13 N N9 C2E . . . D 2 2.908 -82.642 11.444 1 26.31 ? N9 C2E 2256 B 1 HETATM 14 C C8 C2E . . . D 2 2.678 -83.596 12.345 1 29.53 ? C8 C2E 2256 B 1 HETATM 15 N N7 C2E . . . D 2 3.26 -83.237 13.497 1 33.13 ? N7 C2E 2256 B 1 HETATM 16 C C5 C2E . . . D 2 3.859 -82.049 13.303 1 31.36 ? C5 C2E 2256 B 1 HETATM 17 C C6 C2E . . . D 2 4.599 -81.207 14.138 1 30.51 ? C6 C2E 2256 B 1 HETATM 18 O O6 C2E . . . D 2 4.826 -81.547 15.455 1 33.36 ? O6 C2E 2256 B 1 HETATM 19 N N1 C2E . . . D 2 5.078 -80.051 13.643 1 27.74 ? N1 C2E 2256 B 1 HETATM 20 C C2 C2E . . . D 2 4.835 -79.712 12.361 1 30.84 ? C2 C2E 2256 B 1 HETATM 21 N N2 C2E . . . D 2 5.287 -78.447 11.864 1 30.58 ? N2 C2E 2256 B 1 HETATM 22 N N3 C2E . . . D 2 4.125 -80.508 11.54 1 32.53 ? N3 C2E 2256 B 1 HETATM 23 C C4 C2E . . . D 2 3.631 -81.669 11.984 1 30.02 ? C4 C2E 2256 B 1 HETATM 24 P P11 C2E . . . D 2 0.803 -83.582 5.908 1 33.09 ? P11 C2E 2256 B 1 HETATM 25 O O21 C2E . . . D 2 0.438 -85.049 5.898 1 28.52 ? O21 C2E 2256 B 1 HETATM 26 O O11 C2E . . . D 2 1.699 -83.209 4.755 1 30.17 ? O11 C2E 2256 B 1 HETATM 27 O O5A C2E . . . D 2 -0.42 -82.668 5.641 1 32.34 ? O5A C2E 2256 B 1 HETATM 28 C C5A C2E . . . D 2 -1.557 -83.2 6.134 1 31.8 ? C5A C2E 2256 B 1 HETATM 29 C C4A C2E . . . D 2 -2.551 -82.16 6.389 1 29.89 ? C4A C2E 2256 B 1 HETATM 30 O O4A C2E . . . D 2 -3.41 -82.096 5.211 1 27.66 ? O4A C2E 2256 B 1 HETATM 31 C C3A C2E . . . D 2 -3.305 -82.79 7.494 1 30 ? C3A C2E 2256 B 1 HETATM 32 O O3A C2E . . . D 2 -3.106 -82.17 8.708 1 27.52 ? O3A C2E 2256 B 1 HETATM 33 C C2A C2E . . . D 2 -4.688 -82.911 7.027 1 27.53 ? C2A C2E 2256 B 1 HETATM 34 O O2A C2E . . . D 2 -5.49 -81.94 7.522 1 32.58 ? O2A C2E 2256 B 1 HETATM 35 C C1A C2E . . . D 2 -4.565 -82.831 5.531 1 27.7 ? C1A C2E 2256 B 1 HETATM 36 N N91 C2E . . . D 2 -4.759 -84.256 4.85 1 29.54 ? N91 C2E 2256 B 1 HETATM 37 C C81 C2E . . . D 2 -3.898 -85.279 4.973 1 26.77 ? C81 C2E 2256 B 1 HETATM 38 N N71 C2E . . . D 2 -4.425 -86.348 4.367 1 30.63 ? N71 C2E 2256 B 1 HETATM 39 C C51 C2E . . . D 2 -5.644 -86.013 3.863 1 32.99 ? C51 C2E 2256 B 1 HETATM 40 C C61 C2E . . . D 2 -6.639 -86.706 3.144 1 30.56 ? C61 C2E 2256 B 1 HETATM 41 O O61 C2E . . . D 2 -6.506 -88.044 2.826 1 31.54 ? O61 C2E 2256 B 1 HETATM 42 N N11 C2E . . . D 2 -7.757 -86.047 2.794 1 29 ? N11 C2E 2256 B 1 HETATM 43 C C21 C2E . . . D 2 -7.949 -84.752 3.112 1 34.47 ? C21 C2E 2256 B 1 HETATM 44 N N21 C2E . . . D 2 -9.155 -84.089 2.699 1 30.42 ? N21 C2E 2256 B 1 HETATM 45 N N31 C2E . . . D 2 -7.002 -84.078 3.808 1 30.82 ? N31 C2E 2256 B 1 HETATM 46 C C41 C2E . . . D 2 -5.854 -84.671 4.188 1 28.36 ? C41 C2E 2256 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #