data_3PJU # _model_server_result.job_id 7JcyCKbDvaI3vzFiNwl5cA _model_server_result.datetime_utc '2025-03-04 17:29:31' _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 3pju # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2256}' # _entry.id 3PJU # _exptl.entry_id 3PJU _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 120 _cell.entry_id 3PJU _cell.length_a 141.486 _cell.length_b 141.486 _cell.length_c 111.254 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PJU _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_554 x,x-y,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 -18.542333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 3PJU _atom_sites.fract_transf_matrix[1][1] 0.007068 _atom_sites.fract_transf_matrix[1][2] 0.004081 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008161 _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] 0.008988 _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 2256 2256 C2E C2E . C 3 HOH A 1 1 1 HOH HOH . C 3 HOH A 2 2 2 HOH HOH . C 3 HOH A 3 3 3 HOH HOH . C 3 HOH A 4 4 4 HOH HOH . C 3 HOH A 5 5 5 HOH HOH . C 3 HOH A 6 6 6 HOH HOH . C 3 HOH A 7 7 7 HOH HOH . C 3 HOH A 8 8 8 HOH HOH . C 3 HOH A 9 9 9 HOH HOH . C 3 HOH A 10 10 10 HOH HOH . C 3 HOH A 11 11 11 HOH HOH . C 3 HOH A 12 12 12 HOH HOH . C 3 HOH A 13 13 13 HOH HOH . C 3 HOH A 14 14 14 HOH HOH . C 3 HOH A 15 15 15 HOH HOH . C 3 HOH A 16 16 16 HOH HOH . C 3 HOH A 17 17 17 HOH HOH . C 3 HOH A 18 18 18 HOH HOH . C 3 HOH A 19 19 19 HOH HOH . C 3 HOH A 20 20 20 HOH HOH . C 3 HOH A 21 21 21 HOH HOH . C 3 HOH A 22 22 22 HOH HOH . C 3 HOH A 23 23 23 HOH HOH . C 3 HOH A 24 24 24 HOH HOH . C 3 HOH A 25 25 25 HOH HOH . C 3 HOH A 26 26 26 HOH HOH . C 3 HOH A 27 27 27 HOH HOH . C 3 HOH A 28 28 28 HOH HOH . C 3 HOH A 29 29 29 HOH HOH . C 3 HOH A 30 31 31 HOH HOH . C 3 HOH A 31 32 32 HOH HOH . C 3 HOH A 32 33 33 HOH HOH . C 3 HOH A 33 34 34 HOH HOH . C 3 HOH A 34 35 35 HOH HOH . C 3 HOH A 35 36 36 HOH HOH . C 3 HOH A 36 37 37 HOH HOH . C 3 HOH A 37 38 38 HOH HOH . C 3 HOH A 38 39 39 HOH HOH . C 3 HOH A 39 40 40 HOH HOH . C 3 HOH A 40 41 41 HOH HOH . C 3 HOH A 41 42 42 HOH HOH . C 3 HOH A 42 43 43 HOH HOH . C 3 HOH A 43 44 44 HOH HOH . C 3 HOH A 44 45 45 HOH HOH . C 3 HOH A 45 46 46 HOH HOH . C 3 HOH A 46 47 47 HOH HOH . C 3 HOH A 47 48 48 HOH HOH . C 3 HOH A 48 49 49 HOH HOH . C 3 HOH A 49 50 50 HOH HOH . C 3 HOH A 50 51 51 HOH HOH . C 3 HOH A 51 52 52 HOH HOH . C 3 HOH A 52 53 53 HOH HOH . C 3 HOH A 53 54 54 HOH HOH . C 3 HOH A 54 55 55 HOH HOH . C 3 HOH A 55 56 56 HOH HOH . C 3 HOH A 56 57 57 HOH HOH . C 3 HOH A 57 58 58 HOH HOH . C 3 HOH A 58 59 59 HOH HOH . C 3 HOH A 59 60 60 HOH HOH . C 3 HOH A 60 61 61 HOH HOH . C 3 HOH A 61 62 62 HOH HOH . C 3 HOH A 62 63 63 HOH HOH . C 3 HOH A 63 64 64 HOH HOH . C 3 HOH A 64 65 65 HOH HOH . C 3 HOH A 65 66 66 HOH HOH . C 3 HOH A 66 67 67 HOH HOH . C 3 HOH A 67 68 68 HOH HOH . C 3 HOH A 68 69 69 HOH HOH . C 3 HOH A 69 70 70 HOH HOH . C 3 HOH A 70 71 71 HOH HOH . C 3 HOH A 71 72 72 HOH HOH . C 3 HOH A 72 73 73 HOH HOH . C 3 HOH A 73 75 75 HOH HOH . C 3 HOH A 74 76 76 HOH HOH . C 3 HOH A 75 77 77 HOH HOH . C 3 HOH A 76 78 78 HOH HOH . C 3 HOH A 77 79 79 HOH HOH . C 3 HOH A 78 80 80 HOH HOH . C 3 HOH A 79 81 81 HOH HOH . C 3 HOH A 80 82 82 HOH HOH . C 3 HOH A 81 83 83 HOH HOH . C 3 HOH A 82 84 84 HOH HOH . C 3 HOH A 83 85 85 HOH HOH . C 3 HOH A 84 86 86 HOH HOH . C 3 HOH A 85 87 87 HOH HOH . C 3 HOH A 86 88 88 HOH HOH . C 3 HOH A 87 89 89 HOH HOH . C 3 HOH A 88 90 90 HOH HOH . C 3 HOH A 89 91 91 HOH HOH . C 3 HOH A 90 92 92 HOH HOH . C 3 HOH A 91 95 95 HOH HOH . C 3 HOH A 92 100 100 HOH HOH . C 3 HOH A 93 101 101 HOH HOH . C 3 HOH A 94 102 102 HOH HOH . C 3 HOH A 95 649 1 HOH HOH . C 3 HOH A 96 650 2 HOH HOH . C 3 HOH A 97 651 3 HOH HOH . C 3 HOH A 98 652 4 HOH HOH . C 3 HOH A 99 653 8 HOH HOH . C 3 HOH A 100 654 10 HOH HOH . C 3 HOH A 101 655 16 HOH HOH . C 3 HOH A 102 656 18 HOH HOH . C 3 HOH A 103 657 19 HOH HOH . C 3 HOH A 104 658 21 HOH HOH . C 3 HOH A 105 659 22 HOH HOH . C 3 HOH A 106 660 23 HOH HOH . C 3 HOH A 107 661 27 HOH HOH . C 3 HOH A 108 662 28 HOH HOH . C 3 HOH A 109 663 31 HOH HOH . C 3 HOH A 110 664 35 HOH HOH . C 3 HOH A 111 665 38 HOH HOH . C 3 HOH A 112 666 40 HOH HOH . C 3 HOH A 113 667 42 HOH HOH . C 3 HOH A 114 668 43 HOH HOH . C 3 HOH A 115 669 47 HOH HOH . C 3 HOH A 116 670 48 HOH HOH . C 3 HOH A 117 671 49 HOH HOH . C 3 HOH A 118 672 52 HOH HOH . C 3 HOH A 119 673 53 HOH HOH . C 3 HOH A 120 674 55 HOH HOH . C 3 HOH A 121 675 57 HOH HOH . C 3 HOH A 122 676 63 HOH HOH . C 3 HOH A 123 677 84 HOH HOH . C 3 HOH A 124 678 85 HOH HOH . C 3 HOH A 125 679 90 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 29.114 33.484 4.733 1 54.73 ? P1 C2E 2256 A 1 HETATM 2 O O2P C2E . . . B 2 28.868 32.892 6.104 1 47.98 ? O2P C2E 2256 A 1 HETATM 3 O O1P C2E . . . B 2 28.486 32.568 3.703 1 51.1 ? O1P C2E 2256 A 1 HETATM 4 O O5' C2E . . . B 2 28.336 34.869 4.731 1 53.78 ? O5' C2E 2256 A 1 HETATM 5 C C5' C2E . . . B 2 28.056 35.495 3.52 1 47.6 ? C5' C2E 2256 A 1 HETATM 6 C C4' C2E . . . B 2 29.065 36.502 3.037 1 52.95 ? C4' C2E 2256 A 1 HETATM 7 O O4' C2E . . . B 2 28.681 36.954 1.766 1 53.08 ? O4' C2E 2256 A 1 HETATM 8 C C3' C2E . . . B 2 29.145 37.767 3.859 1 52.38 ? C3' C2E 2256 A 1 HETATM 9 O O3' C2E . . . B 2 30.315 38.463 3.566 1 48.25 ? O3' C2E 2256 A 1 HETATM 10 C C2' C2E . . . B 2 28.033 38.48 3.375 1 50.67 ? C2' C2E 2256 A 1 HETATM 11 O O2' C2E . . . B 2 28.092 39.903 3.538 1 48.92 ? O2' C2E 2256 A 1 HETATM 12 C C1' C2E . . . B 2 27.936 38.122 1.971 1 46.51 ? C1' C2E 2256 A 1 HETATM 13 N N9 C2E . . . B 2 26.497 37.958 1.346 1 45.01 ? N9 C2E 2256 A 1 HETATM 14 C C8 C2E . . . B 2 25.403 37.584 2.044 1 42.9 ? C8 C2E 2256 A 1 HETATM 15 N N7 C2E . . . B 2 24.382 37.489 1.179 1 43.49 ? N7 C2E 2256 A 1 HETATM 16 C C5 C2E . . . B 2 24.845 37.787 -0.059 1 43.45 ? C5 C2E 2256 A 1 HETATM 17 C C6 C2E . . . B 2 24.224 37.842 -1.309 1 43.26 ? C6 C2E 2256 A 1 HETATM 18 O O6 C2E . . . B 2 22.866 37.58 -1.445 1 46.2 ? O6 C2E 2256 A 1 HETATM 19 N N1 C2E . . . B 2 24.974 38.195 -2.374 1 43.03 ? N1 C2E 2256 A 1 HETATM 20 C C2 C2E . . . B 2 26.286 38.477 -2.253 1 44.42 ? C2 C2E 2256 A 1 HETATM 21 N N2 C2E . . . B 2 27.018 38.832 -3.433 1 39.87 ? N2 C2E 2256 A 1 HETATM 22 N N3 C2E . . . B 2 26.913 38.423 -1.061 1 42.35 ? N3 C2E 2256 A 1 HETATM 23 C C4 C2E . . . B 2 26.214 38.091 0.042 1 44.31 ? C4 C2E 2256 A 1 HETATM 24 P P11 C2E . . . B 2 31.435 38.531 4.67 1 50.15 ? P11 C2E 2256 A 1 HETATM 25 O O21 C2E . . . B 2 30.809 38.599 6.045 1 42.9 ? O21 C2E 2256 A 1 HETATM 26 O O11 C2E . . . B 2 32.401 39.674 4.488 1 48.07 ? O11 C2E 2256 A 1 HETATM 27 O O5A C2E . . . B 2 32.378 37.313 4.531 1 51.56 ? O5A C2E 2256 A 1 HETATM 28 C C5A C2E . . . B 2 31.966 36.329 5.359 1 47.88 ? C5A C2E 2256 A 1 HETATM 29 C C4A C2E . . . B 2 32.476 35.05 4.886 1 51.46 ? C4A C2E 2256 A 1 HETATM 30 O O4A C2E . . . B 2 33.757 34.898 5.57 1 47.64 ? O4A C2E 2256 A 1 HETATM 31 C C3A C2E . . . B 2 31.487 34.079 5.411 1 52.07 ? C3A C2E 2256 A 1 HETATM 32 O O3A C2E . . . B 2 30.659 33.522 4.431 1 44.83 ? O3A C2E 2256 A 1 HETATM 33 C C2A C2E . . . B 2 32.288 33.183 6.263 1 45.89 ? C2A C2E 2256 A 1 HETATM 34 O O2A C2E . . . B 2 32.569 32.02 5.62 1 49.68 ? O2A C2E 2256 A 1 HETATM 35 C C1A C2E . . . B 2 33.532 34 6.612 1 44.32 ? C1A C2E 2256 A 1 HETATM 36 N N91 C2E . . . B 2 33.532 34.556 8.102 1 39.87 ? N91 C2E 2256 A 1 HETATM 37 C C81 C2E . . . B 2 32.695 35.498 8.571 1 44.23 ? C81 C2E 2256 A 1 HETATM 38 N N71 C2E . . . B 2 32.798 35.573 9.91 1 42.83 ? N71 C2E 2256 A 1 HETATM 39 C C51 C2E . . . B 2 33.711 34.657 10.301 1 44.54 ? C51 C2E 2256 A 1 HETATM 40 C C61 C2E . . . B 2 34.234 34.277 11.538 1 43.48 ? C61 C2E 2256 A 1 HETATM 41 O O61 C2E . . . B 2 33.777 34.869 12.696 1 45.44 ? O61 C2E 2256 A 1 HETATM 42 N N11 C2E . . . B 2 35.158 33.29 11.583 1 43.97 ? N11 C2E 2256 A 1 HETATM 43 C C21 C2E . . . B 2 35.589 32.671 10.477 1 46.19 ? C21 C2E 2256 A 1 HETATM 44 N N21 C2E . . . B 2 36.616 31.681 10.556 1 48.27 ? N21 C2E 2256 A 1 HETATM 45 N N31 C2E . . . B 2 35.089 33.03 9.281 1 50.67 ? N31 C2E 2256 A 1 HETATM 46 C C41 C2E . . . B 2 34.164 34.004 9.152 1 43.81 ? C41 C2E 2256 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #