data_4H54 # _model_server_result.job_id YJyDkoF0HBNO6XwbLma_AA _model_server_result.datetime_utc '2024-11-25 17:03:11' _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 4h54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":405}' # _entry.id 4H54 # _exptl.entry_id 4H54 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 5 _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 4H54 _cell.length_a 102.593 _cell.length_b 102.593 _cell.length_c 129.156 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4H54 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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,G,H,I,J,K _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 NE2 HIS 22 A HIS 22 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc2 A NE2 HIS 79 A HIS 79 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc3 A NE2 HIS 83 A HIS 83 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc4 A OD2 ASP 165 A ASP 165 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.727 ? metalc ? metalc5 A O ILE 166 A ILE 166 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc6 A OE2 GLU 208 A GLU 208 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc7 A OE1 GLU 208 A GLU 208 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc8 D O3G GAV . A GAV 402 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc9 D O2B GAV . A GAV 402 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc10 B NE2 HIS 22 B HIS 22 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc11 B NE2 HIS 79 B HIS 79 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc12 B NE2 HIS 83 B HIS 83 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc13 B OD2 ASP 165 B ASP 165 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc14 B O ILE 166 B ILE 166 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.677 ? metalc ? metalc15 B OE1 GLU 208 B GLU 208 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc16 B OE2 GLU 208 B GLU 208 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc17 I O2B GAV . B GAV 402 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc18 I O3B GAV . B GAV 402 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc19 I O3G GAV . B GAV 402 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.672 ? # _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 4H54 _atom_sites.fract_transf_matrix[1][1] 0.009747 _atom_sites.fract_transf_matrix[1][2] 0.005628 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011255 _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] 0.007743 _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 ZN A 1 401 400 ZN ZN . D 3 GAV A 1 402 600 GAV GAV . E 4 MG A 1 403 601 MG MG . F 3 GAV A 1 404 700 GAV GAV . G 5 C2E A 1 405 701 C2E C2E . H 2 ZN B 1 401 400 ZN ZN . I 3 GAV B 1 402 600 GAV GAV . J 4 MG B 1 403 601 MG MG . K 3 GAV B 1 404 700 GAV GAV . # 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 . . . G 5 42.811 -47.827 18.308 1 61.99 ? P1 C2E 405 A 1 HETATM 2 O O2P C2E . . . G 5 42.8 -49.073 17.459 1 66.29 ? O2P C2E 405 A 1 HETATM 3 O O1P C2E . . . G 5 43.181 -46.497 17.697 1 50.78 ? O1P C2E 405 A 1 HETATM 4 O O5' C2E . . . G 5 41.347 -47.664 18.968 1 53.07 ? O5' C2E 405 A 1 HETATM 5 C C5' C2E . . . G 5 40.848 -46.338 19.148 1 42.71 ? C5' C2E 405 A 1 HETATM 6 C C4' C2E . . . G 5 39.616 -46.197 20.048 1 42.23 ? C4' C2E 405 A 1 HETATM 7 O O4' C2E . . . G 5 38.399 -46.442 19.33 1 33.19 ? O4' C2E 405 A 1 HETATM 8 C C3' C2E . . . G 5 39.587 -47.087 21.283 1 59.7 ? C3' C2E 405 A 1 HETATM 9 O O3' C2E . . . G 5 40.335 -46.521 22.355 1 74.51 ? O3' C2E 405 A 1 HETATM 10 C C2' C2E . . . G 5 38.101 -47.16 21.565 1 53.97 ? C2' C2E 405 A 1 HETATM 11 O O2' C2E . . . G 5 37.678 -46.05 22.365 1 53.78 ? O2' C2E 405 A 1 HETATM 12 C C1' C2E . . . G 5 37.455 -47.092 20.187 1 37.75 ? C1' C2E 405 A 1 HETATM 13 N N9 C2E . . . G 5 37.172 -48.443 19.632 1 38.14 ? N9 C2E 405 A 1 HETATM 14 C C8 C2E . . . G 5 37.875 -49.026 18.642 1 36.27 ? C8 C2E 405 A 1 HETATM 15 N N7 C2E . . . G 5 37.37 -50.25 18.354 1 38.47 ? N7 C2E 405 A 1 HETATM 16 C C5 C2E . . . G 5 36.323 -50.472 19.162 1 42.83 ? C5 C2E 405 A 1 HETATM 17 C C6 C2E . . . G 5 35.353 -51.575 19.37 1 52.05 ? C6 C2E 405 A 1 HETATM 18 O O6 C2E . . . G 5 35.399 -52.623 18.689 1 56.98 ? O6 C2E 405 A 1 HETATM 19 N N1 C2E . . . G 5 34.419 -51.422 20.311 1 59.5 ? N1 C2E 405 A 1 HETATM 20 C C2 C2E . . . G 5 34.348 -50.301 21.057 1 56.59 ? C2 C2E 405 A 1 HETATM 21 N N2 C2E . . . G 5 33.372 -50.218 21.99 1 66.59 ? N2 C2E 405 A 1 HETATM 22 N N3 C2E . . . G 5 35.2 -49.249 20.921 1 46.87 ? N3 C2E 405 A 1 HETATM 23 C C4 C2E . . . G 5 36.194 -49.276 20.005 1 41.53 ? C4 C2E 405 A 1 HETATM 24 P P11 C2E . . . G 5 40.965 -47.45 23.499 1 111.46 ? P11 C2E 405 A 1 HETATM 25 O O21 C2E . . . G 5 39.874 -48.338 24.033 1 124.63 ? O21 C2E 405 A 1 HETATM 26 O O11 C2E . . . G 5 41.756 -46.564 24.426 1 133.33 ? O11 C2E 405 A 1 HETATM 27 O O5A C2E . . . G 5 41.987 -48.382 22.696 1 134.77 ? O5A C2E 405 A 1 HETATM 28 C C5A C2E . . . G 5 43.37 -48.069 22.699 1 148.37 ? C5A C2E 405 A 1 HETATM 29 C C4A C2E . . . G 5 44.102 -49.045 21.802 1 148.97 ? C4A C2E 405 A 1 HETATM 30 O O4A C2E . . . G 5 44.082 -50.372 22.33 1 156.58 ? O4A C2E 405 A 1 HETATM 31 C C3A C2E . . . G 5 43.45 -49.171 20.445 1 125.05 ? C3A C2E 405 A 1 HETATM 32 O O3A C2E . . . G 5 43.771 -48.097 19.574 1 91.27 ? O3A C2E 405 A 1 HETATM 33 C C2A C2E . . . G 5 43.974 -50.501 19.969 1 137.08 ? C2A C2E 405 A 1 HETATM 34 O O2A C2E . . . G 5 45.271 -50.376 19.39 1 141.98 ? O2A C2E 405 A 1 HETATM 35 C C1A C2E . . . G 5 44.02 -51.311 21.25 1 147.87 ? C1A C2E 405 A 1 HETATM 36 N N91 C2E . . . G 5 42.78 -52.114 21.279 1 142.96 ? N91 C2E 405 A 1 HETATM 37 C C81 C2E . . . G 5 41.669 -51.866 21.991 1 141.31 ? C81 C2E 405 A 1 HETATM 38 N N71 C2E . . . G 5 40.728 -52.813 21.745 1 143.96 ? N71 C2E 405 A 1 HETATM 39 C C51 C2E . . . G 5 41.237 -53.673 20.849 1 145.04 ? C51 C2E 405 A 1 HETATM 40 C C61 C2E . . . G 5 40.782 -54.899 20.157 1 243.64 ? C61 C2E 405 A 1 HETATM 41 O O61 C2E . . . G 5 39.645 -55.365 20.366 1 252.3 ? O61 C2E 405 A 1 HETATM 42 N N11 C2E . . . G 5 41.623 -55.494 19.301 1 270.9 ? N11 C2E 405 A 1 HETATM 43 C C21 C2E . . . G 5 42.856 -55.006 19.063 1 272.35 ? C21 C2E 405 A 1 HETATM 44 N N21 C2E . . . G 5 43.663 -55.648 18.188 1 277.25 ? N21 C2E 405 A 1 HETATM 45 N N31 C2E . . . G 5 43.337 -53.891 19.663 1 147.3 ? N31 C2E 405 A 1 HETATM 46 C C41 C2E . . . G 5 42.588 -53.203 20.547 1 142.29 ? C41 C2E 405 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 46 #