data_3BRE # _model_server_result.job_id 5fOtoE8hGU4YJOzivhxunA _model_server_result.datetime_utc '2024-11-05 00:41:24' _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 3bre # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":360}' # _entry.id 3BRE # _exptl.entry_id 3BRE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 3 _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.79 _cell.angle_gamma 90 _cell.entry_id 3BRE _cell.length_a 144.51 _cell.length_b 72.748 _cell.length_c 106.095 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BRE _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 ? tetrameric 4 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 G N N ? 3 H N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OD2 _struct_conn.ptnr1_label_comp_id ASP _struct_conn.ptnr1_label_seq_id 70 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ASP _struct_conn.ptnr1_auth_seq_id 70 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id MG _struct_conn.ptnr2_label_comp_id MG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id MG _struct_conn.ptnr2_auth_seq_id 359 _struct_conn.ptnr2_symmetry 1_555 _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 2.461 _struct_conn.pdbx_value_order ? # _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 3BRE _atom_sites.fract_transf_matrix[1][1] 0.00692 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002628 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013746 _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] 0.010082 _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 MG A 1 359 2 MG MG . D 3 C2E A 1 360 3 C2E C2E . E 3 C2E A 1 361 4 C2E C2E . F 2 MG B 1 359 1 MG MG . G 3 C2E B 1 360 1 C2E C2E . H 3 C2E B 1 361 2 C2E C2E . # 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 3 33.221 15.765 -16.806 1 54.06 ? P1 C2E 360 A 1 HETATM 2 O O2P C2E . . . D 3 34.556 16.31 -17.298 1 52.56 ? O2P C2E 360 A 1 HETATM 3 O O1P C2E . . . D 3 32.528 16.777 -15.926 1 55.6 ? O1P C2E 360 A 1 HETATM 4 O O5' C2E . . . D 3 33.461 14.433 -15.975 1 53.74 ? O5' C2E 360 A 1 HETATM 5 C C5' C2E . . . D 3 34.105 13.35 -16.612 1 55.18 ? C5' C2E 360 A 1 HETATM 6 C C4' C2E . . . D 3 34.038 12.126 -15.731 1 56.42 ? C4' C2E 360 A 1 HETATM 7 O O4' C2E . . . D 3 34.497 12.49 -14.434 1 59.1 ? O4' C2E 360 A 1 HETATM 8 C C3' C2E . . . D 3 32.648 11.515 -15.521 1 57.08 ? C3' C2E 360 A 1 HETATM 9 O O3' C2E . . . D 3 32.435 10.655 -16.636 1 56.54 ? O3' C2E 360 A 1 HETATM 10 C C2' C2E . . . D 3 32.868 10.844 -14.187 1 58.23 ? C2' C2E 360 A 1 HETATM 11 O O2' C2E . . . D 3 33.43 9.541 -14.355 1 58.09 ? O2' C2E 360 A 1 HETATM 12 C C1' C2E . . . D 3 33.829 11.738 -13.402 1 59.26 ? C1' C2E 360 A 1 HETATM 13 N N9 C2E . . . D 3 33.08 12.691 -12.527 1 60.67 ? N9 C2E 360 A 1 HETATM 14 C C8 C2E . . . D 3 32.985 14.04 -12.671 1 60.04 ? C8 C2E 360 A 1 HETATM 15 N N7 C2E . . . D 3 32.213 14.586 -11.693 1 58.03 ? N7 C2E 360 A 1 HETATM 16 C C5 C2E . . . D 3 31.804 13.592 -10.903 1 59.77 ? C5 C2E 360 A 1 HETATM 17 C C6 C2E . . . D 3 30.959 13.46 -9.677 1 60.91 ? C6 C2E 360 A 1 HETATM 18 O O6 C2E . . . D 3 30.433 14.467 -9.148 1 60.97 ? O6 C2E 360 A 1 HETATM 19 N N1 C2E . . . D 3 30.78 12.22 -9.149 1 59.96 ? N1 C2E 360 A 1 HETATM 20 C C2 C2E . . . D 3 31.349 11.1 -9.713 1 59.14 ? C2 C2E 360 A 1 HETATM 21 N N2 C2E . . . D 3 31.151 9.893 -9.155 1 58.76 ? N2 C2E 360 A 1 HETATM 22 N N3 C2E . . . D 3 32.122 11.16 -10.833 1 56.87 ? N3 C2E 360 A 1 HETATM 23 C C4 C2E . . . D 3 32.377 12.341 -11.451 1 58.74 ? C4 C2E 360 A 1 HETATM 24 P P11 C2E . . . D 3 30.925 10.586 -17.14 1 55.59 ? P11 C2E 360 A 1 HETATM 25 O O21 C2E . . . D 3 30.884 9.628 -18.327 1 56.46 ? O21 C2E 360 A 1 HETATM 26 O O11 C2E . . . D 3 30.026 10.105 -16.031 1 55.63 ? O11 C2E 360 A 1 HETATM 27 O O5A C2E . . . D 3 30.461 11.998 -17.683 1 57.1 ? O5A C2E 360 A 1 HETATM 28 C C5A C2E . . . D 3 31.207 12.589 -18.741 1 55.76 ? C5A C2E 360 A 1 HETATM 29 C C4A C2E . . . D 3 30.671 13.975 -18.959 1 53.72 ? C4A C2E 360 A 1 HETATM 30 O O4A C2E . . . D 3 29.242 13.906 -18.998 1 54.02 ? O4A C2E 360 A 1 HETATM 31 C C3A C2E . . . D 3 31.03 14.959 -17.844 1 53.29 ? C3A C2E 360 A 1 HETATM 32 O O3A C2E . . . D 3 32.337 15.487 -18.119 1 52.48 ? O3A C2E 360 A 1 HETATM 33 C C2A C2E . . . D 3 29.842 15.912 -17.964 1 51.33 ? C2A C2E 360 A 1 HETATM 34 O O2A C2E . . . D 3 30.098 16.934 -18.941 1 45.57 ? O2A C2E 360 A 1 HETATM 35 C C1A C2E . . . D 3 28.66 15.052 -18.394 1 49.26 ? C1A C2E 360 A 1 HETATM 36 N N91 C2E . . . D 3 27.832 14.65 -17.201 1 48.74 ? N91 C2E 360 A 1 HETATM 37 C C81 C2E . . . D 3 27.639 13.414 -16.69 1 48.7 ? C81 C2E 360 A 1 HETATM 38 N N71 C2E . . . D 3 26.796 13.446 -15.61 1 47.57 ? N71 C2E 360 A 1 HETATM 39 C C51 C2E . . . D 3 26.428 14.718 -15.416 1 47.18 ? C51 C2E 360 A 1 HETATM 40 C C61 C2E . . . D 3 25.549 15.482 -14.479 1 47.29 ? C61 C2E 360 A 1 HETATM 41 O O61 C2E . . . D 3 24.892 14.932 -13.545 1 47.85 ? O61 C2E 360 A 1 HETATM 42 N N11 C2E . . . D 3 25.462 16.824 -14.658 1 47.6 ? N11 C2E 360 A 1 HETATM 43 C C21 C2E . . . D 3 26.127 17.498 -15.632 1 48.11 ? C21 C2E 360 A 1 HETATM 44 N N21 C2E . . . D 3 25.988 18.838 -15.744 1 44.19 ? N21 C2E 360 A 1 HETATM 45 N N31 C2E . . . D 3 26.939 16.867 -16.517 1 48.9 ? N31 C2E 360 A 1 HETATM 46 C C41 C2E . . . D 3 27.12 15.508 -16.458 1 49.5 ? C41 C2E 360 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #