data_6ZXM # _model_server_result.job_id DwWZQyzo7IxEhj7loTGQNA _model_server_result.datetime_utc '2024-12-01 07:12:13' _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":"T","auth_seq_id":302}' # _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 . . . T 2 -22.495 17.419 33.354 1 76.26 ? P1 C2E 302 E 1 HETATM 2 O O2P C2E . . . T 2 -23.273 17.646 34.629 1 73.42 ? O2P C2E 302 E 1 HETATM 3 O O1P C2E . . . T 2 -22.168 18.6 32.476 1 79.14 ? O1P C2E 302 E 1 HETATM 4 O O5' C2E . . . T 2 -21.019 16.763 33.449 1 75.69 ? O5' C2E 302 E 1 HETATM 5 C C5' C2E . . . T 2 -20.212 16.618 32.266 1 74.68 ? C5' C2E 302 E 1 HETATM 6 C C4' C2E . . . T 2 -19.399 15.356 32.352 1 74.9 ? C4' C2E 302 E 1 HETATM 7 O O4' C2E . . . T 2 -18.395 15.521 33.384 1 78.45 ? O4' C2E 302 E 1 HETATM 8 C C3' C2E . . . T 2 -20.1 14.088 32.816 1 75.57 ? C3' C2E 302 E 1 HETATM 9 O O3' C2E . . . T 2 -20.888 13.348 31.818 1 75.27 ? O3' C2E 302 E 1 HETATM 10 C C2' C2E . . . T 2 -18.874 13.223 33.225 1 78.25 ? C2' C2E 302 E 1 HETATM 11 O O2' C2E . . . T 2 -18.313 12.394 32.177 1 78.7 ? O2' C2E 302 E 1 HETATM 12 C C1' C2E . . . T 2 -17.82 14.252 33.642 1 82.78 ? C1' C2E 302 E 1 HETATM 13 N N9 C2E . . . T 2 -17.372 14.12 35.049 1 91.04 ? N9 C2E 302 E 1 HETATM 14 C C8 C2E . . . T 2 -16.453 13.22 35.574 1 93.62 ? C8 C2E 302 E 1 HETATM 15 N N7 C2E . . . T 2 -16.268 13.33 36.88 1 91.87 ? N7 C2E 302 E 1 HETATM 16 C C5 C2E . . . T 2 -17.083 14.4 37.237 1 93.16 ? C5 C2E 302 E 1 HETATM 17 C C6 C2E . . . T 2 -17.292 15.014 38.502 1 96.53 ? C6 C2E 302 E 1 HETATM 18 O O6 C2E . . . T 2 -16.78 14.744 39.605 1 95.57 ? O6 C2E 302 E 1 HETATM 19 N N1 C2E . . . T 2 -18.185 16.088 38.381 1 101 ? N1 C2E 302 E 1 HETATM 20 C C2 C2E . . . T 2 -18.834 16.488 37.227 1 100.47 ? C2 C2E 302 E 1 HETATM 21 N N2 C2E . . . T 2 -19.695 17.521 37.312 1 104.99 ? N2 C2E 302 E 1 HETATM 22 N N3 C2E . . . T 2 -18.652 15.902 36.05 1 93.62 ? N3 C2E 302 E 1 HETATM 23 C C4 C2E . . . T 2 -17.769 14.882 36.127 1 92.22 ? C4 C2E 302 E 1 HETATM 24 P P11 C2E . . . T 2 -21.632 12.047 32.484 1 76.05 ? P11 C2E 302 E 1 HETATM 25 O O21 C2E . . . T 2 -20.909 11.178 33.548 1 75.48 ? O21 C2E 302 E 1 HETATM 26 O O11 C2E . . . T 2 -22.44 11.155 31.529 1 77.7 ? O11 C2E 302 E 1 HETATM 27 O O5A C2E . . . T 2 -22.819 12.85 33.204 1 75.2 ? O5A C2E 302 E 1 HETATM 28 C C5A C2E . . . T 2 -23.918 13.178 32.289 1 76.82 ? C5A C2E 302 E 1 HETATM 29 C C4A C2E . . . T 2 -24.738 14.318 32.844 1 77.5 ? C4A C2E 302 E 1 HETATM 30 O O4A C2E . . . T 2 -25.708 13.81 33.798 1 76.27 ? O4A C2E 302 E 1 HETATM 31 C C3A C2E . . . T 2 -23.936 15.388 33.589 1 77.59 ? C3A C2E 302 E 1 HETATM 32 O O3A C2E . . . T 2 -23.358 16.284 32.633 1 75.71 ? O3A C2E 302 E 1 HETATM 33 C C2A C2E . . . T 2 -25.028 15.952 34.49 1 79.41 ? C2A C2E 302 E 1 HETATM 34 O O2A C2E . . . T 2 -25.862 16.837 33.765 1 79.36 ? O2A C2E 302 E 1 HETATM 35 C C1A C2E . . . T 2 -25.671 14.634 34.95 1 79.31 ? C1A C2E 302 E 1 HETATM 36 N N91 C2E . . . T 2 -24.934 13.969 36.058 1 81.41 ? N91 C2E 302 E 1 HETATM 37 C C81 C2E . . . T 2 -24.052 12.891 36.049 1 81.14 ? C81 C2E 302 E 1 HETATM 38 N N71 C2E . . . T 2 -23.561 12.561 37.242 1 81.16 ? N71 C2E 302 E 1 HETATM 39 C C51 C2E . . . T 2 -24.13 13.502 38.096 1 81.93 ? C51 C2E 302 E 1 HETATM 40 C C61 C2E . . . T 2 -23.983 13.672 39.497 1 78.55 ? C61 C2E 302 E 1 HETATM 41 O O61 C2E . . . T 2 -23.292 12.996 40.299 1 75.44 ? O61 C2E 302 E 1 HETATM 42 N N11 C2E . . . T 2 -24.749 14.771 39.934 1 78.33 ? N11 C2E 302 E 1 HETATM 43 C C21 C2E . . . T 2 -25.548 15.586 39.132 1 79.48 ? C21 C2E 302 E 1 HETATM 44 N N21 C2E . . . T 2 -26.162 16.629 39.703 1 81.28 ? N21 C2E 302 E 1 HETATM 45 N N31 C2E . . . T 2 -25.729 15.406 37.834 1 80.34 ? N31 C2E 302 E 1 HETATM 46 C C41 C2E . . . T 2 -24.98 14.363 37.378 1 82.68 ? C41 C2E 302 E 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 547 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #