data_6ZXM # _model_server_result.job_id 4Vv9TJxTNOBRfqVDL0Dvpg _model_server_result.datetime_utc '2024-12-01 07:11:49' _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 6zxm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":301}' # _entry.id 6ZXM # _exptl.entry_id 6ZXM _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 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 118.2 _cell.angle_gamma 90 _cell.entry_id 6ZXM _cell.length_a 122.603 _cell.length_b 72.917 _cell.length_c 125.729 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZXM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,K,L 1 1 C,D,M,N,O,P,Q,R 2 1 E,F,S,T,U,V,W,X 3 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 G N N ? 2 H N N ? 2 J N N ? 2 K N N ? 2 M N N ? 2 N N N ? 2 P N N ? 2 Q N N ? 2 S N N ? 2 T N N ? 2 V N N ? 2 W N 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 OE2 GLU 32 A GLU 12 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc2 A OD1 ASP 33 A ASP 13 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc3 A OD2 ASP 76 A ASP 56 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc4 B OE2 GLU 32 B GLU 12 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc5 B OD1 ASP 33 B ASP 13 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc6 B OD2 ASP 76 B ASP 56 1_555 L MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc7 L MG MG . B MG 303 1_555 F O GLY 107 F GLY 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc8 C OE2 GLU 32 C GLU 12 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc9 C OD1 ASP 33 C ASP 13 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc10 C OD2 ASP 76 C ASP 56 1_555 O MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc11 D OE2 GLU 32 D GLU 12 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc12 D OD1 ASP 33 D ASP 13 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc13 D OD2 ASP 76 D ASP 56 1_555 R MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc14 E OE2 GLU 32 E GLU 12 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc15 E OD1 ASP 33 E ASP 13 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc16 E OD2 ASP 76 E ASP 56 1_555 U MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc17 F OE2 GLU 32 F GLU 12 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc18 F OD1 ASP 33 F ASP 13 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc19 F OD2 ASP 76 F ASP 56 1_555 X MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? # _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 6ZXM _atom_sites.fract_transf_matrix[1][1] 0.008156 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004374 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013714 _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] 0.009025 _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 G 2 C2E A 1 301 301 C2E C2E . H 2 C2E A 1 302 302 C2E C2E . I 3 MG A 1 303 303 MG MG . J 2 C2E B 1 301 301 C2E C2E . K 2 C2E B 1 302 302 C2E C2E . L 3 MG B 1 303 303 MG MG . M 2 C2E C 1 301 301 C2E C2E . N 2 C2E C 1 302 302 C2E C2E . O 3 MG C 1 303 303 MG MG . P 2 C2E D 1 301 301 C2E C2E . Q 2 C2E D 1 302 302 C2E C2E . R 3 MG D 1 303 303 MG MG . S 2 C2E E 1 301 301 C2E C2E . T 2 C2E E 1 302 302 C2E C2E . U 3 MG E 1 303 303 MG MG . V 2 C2E F 1 301 301 C2E C2E . W 2 C2E F 1 302 302 C2E C2E . X 3 MG F 1 303 303 MG MG . # 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 . . . S 2 -20.545 10.469 43.586 1 62.75 ? P1 C2E 301 E 1 HETATM 2 O O2P C2E . . . S 2 -20.85 10.272 42.129 1 62.04 ? O2P C2E 301 E 1 HETATM 3 O O1P C2E . . . S 2 -19.571 9.536 44.239 1 64.47 ? O1P C2E 301 E 1 HETATM 4 O O5' C2E . . . S 2 -20.303 12.054 43.859 1 63.7 ? O5' C2E 301 E 1 HETATM 5 C C5' C2E . . . S 2 -21.199 12.891 43.116 1 64.64 ? C5' C2E 301 E 1 HETATM 6 C C4' C2E . . . S 2 -21.37 14.263 43.706 1 69.01 ? C4' C2E 301 E 1 HETATM 7 O O4' C2E . . . S 2 -20.275 15.079 43.251 1 73.05 ? O4' C2E 301 E 1 HETATM 8 C C3' C2E . . . S 2 -22.643 14.979 43.21 1 71.65 ? C3' C2E 301 E 1 HETATM 9 O O3' C2E . . . S 2 -23.759 15.105 44.129 1 72.05 ? O3' C2E 301 E 1 HETATM 10 C C2' C2E . . . S 2 -22.123 16.339 42.728 1 76.28 ? C2' C2E 301 E 1 HETATM 11 O O2' C2E . . . S 2 -22.038 17.366 43.697 1 78.81 ? O2' C2E 301 E 1 HETATM 12 C C1' C2E . . . S 2 -20.742 15.933 42.22 1 78.82 ? C1' C2E 301 E 1 HETATM 13 N N9 C2E . . . S 2 -20.754 15.251 40.892 1 83.95 ? N9 C2E 301 E 1 HETATM 14 C C8 C2E . . . S 2 -20.174 14.021 40.65 1 87.3 ? C8 C2E 301 E 1 HETATM 15 N N7 C2E . . . S 2 -20.33 13.571 39.414 1 87.7 ? N7 C2E 301 E 1 HETATM 16 C C5 C2E . . . S 2 -21.039 14.582 38.771 1 86.68 ? C5 C2E 301 E 1 HETATM 17 C C6 C2E . . . S 2 -21.512 14.637 37.416 1 83.15 ? C6 C2E 301 E 1 HETATM 18 O O6 C2E . . . S 2 -21.339 13.793 36.533 1 79.81 ? O6 C2E 301 E 1 HETATM 19 N N1 C2E . . . S 2 -22.18 15.831 37.139 1 83.15 ? N1 C2E 301 E 1 HETATM 20 C C2 C2E . . . S 2 -22.355 16.829 38.055 1 85.39 ? C2 C2E 301 E 1 HETATM 21 N N2 C2E . . . S 2 -22.951 17.917 37.582 1 87.69 ? N2 C2E 301 E 1 HETATM 22 N N3 C2E . . . S 2 -21.957 16.783 39.34 1 86.38 ? N3 C2E 301 E 1 HETATM 23 C C4 C2E . . . S 2 -21.301 15.63 39.649 1 86.49 ? C4 C2E 301 E 1 HETATM 24 P P11 C2E . . . S 2 -24.882 13.963 43.872 1 71.02 ? P11 C2E 301 E 1 HETATM 25 O O21 C2E . . . S 2 -25.273 13.899 42.416 1 73.14 ? O21 C2E 301 E 1 HETATM 26 O O11 C2E . . . S 2 -26.057 14.121 44.791 1 71.24 ? O11 C2E 301 E 1 HETATM 27 O O5A C2E . . . S 2 -24.151 12.529 44.032 1 66.35 ? O5A C2E 301 E 1 HETATM 28 C C5A C2E . . . S 2 -24.478 11.517 44.988 1 63.45 ? C5A C2E 301 E 1 HETATM 29 C C4A C2E . . . S 2 -24.158 10.177 44.387 1 61.05 ? C4A C2E 301 E 1 HETATM 30 O O4A C2E . . . S 2 -25.256 9.78 43.551 1 59.13 ? O4A C2E 301 E 1 HETATM 31 C C3A C2E . . . S 2 -22.962 10.141 43.463 1 60.76 ? C3A C2E 301 E 1 HETATM 32 O O3A C2E . . . S 2 -21.861 9.925 44.313 1 61.73 ? O3A C2E 301 E 1 HETATM 33 C C2A C2E . . . S 2 -23.259 8.975 42.523 1 58.47 ? C2A C2E 301 E 1 HETATM 34 O O2A C2E . . . S 2 -22.743 7.805 43.136 1 58.31 ? O2A C2E 301 E 1 HETATM 35 C C1A C2E . . . S 2 -24.79 9.04 42.451 1 58.17 ? C1A C2E 301 E 1 HETATM 36 N N91 C2E . . . S 2 -25.429 9.681 41.248 1 58.91 ? N91 C2E 301 E 1 HETATM 37 C C81 C2E . . . S 2 -25.851 10.972 41.004 1 59.9 ? C81 C2E 301 E 1 HETATM 38 N N71 C2E . . . S 2 -26.368 11.132 39.784 1 59.93 ? N71 C2E 301 E 1 HETATM 39 C C51 C2E . . . S 2 -26.192 9.872 39.197 1 58.89 ? C51 C2E 301 E 1 HETATM 40 C C61 C2E . . . S 2 -26.482 9.395 37.899 1 58.07 ? C61 C2E 301 E 1 HETATM 41 O O61 C2E . . . S 2 -26.939 10.02 36.934 1 60.58 ? O61 C2E 301 E 1 HETATM 42 N N11 C2E . . . S 2 -26.101 8.061 37.755 1 57 ? N11 C2E 301 E 1 HETATM 43 C C21 C2E . . . S 2 -25.595 7.246 38.723 1 56.19 ? C21 C2E 301 E 1 HETATM 44 N N21 C2E . . . S 2 -25.284 5.978 38.404 1 55.57 ? N21 C2E 301 E 1 HETATM 45 N N31 C2E . . . S 2 -25.367 7.672 39.946 1 57.24 ? N31 C2E 301 E 1 HETATM 46 C C41 C2E . . . S 2 -25.672 8.981 40.092 1 58.56 ? C41 C2E 301 E 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #