data_3D45 # _model_server_result.job_id QyVJFXUe2mjwdmCaFMkg2w _model_server_result.datetime_utc '2024-11-20 07:32:07' _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 3d45 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":651}' # _entry.id 3D45 # _exptl.entry_id 3D45 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 379.263 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 3D45 _cell.length_a 58.013 _cell.length_b 128.35 _cell.length_c 176.844 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D45 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _chem_comp.formula 'C11 H18 N5 O8 P' _chem_comp.formula_weight 379.263 _chem_comp.id 7MG _chem_comp.mon_nstd_flag n _chem_comp.name "7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 P OP1 7MG doub 1 n n P OP2 7MG sing 2 n n P OP3 7MG sing 3 n n P O5' 7MG sing 4 n n OP2 HOP2 7MG sing 5 n n OP3 HOP3 7MG sing 6 n n O5' C5' 7MG sing 7 n n C5' C4' 7MG sing 8 n n C5' H5' 7MG sing 9 n n C5' "H5''" 7MG sing 10 n n C4' O4' 7MG sing 11 n n C4' C3' 7MG sing 12 n n C4' H4' 7MG sing 13 n n O4' C1' 7MG sing 14 n n C3' O3' 7MG sing 15 n n C3' C2' 7MG sing 16 n n C3' H3' 7MG sing 17 n n O3' HO3' 7MG sing 18 n n C2' O2' 7MG sing 19 n n C2' C1' 7MG sing 20 n n C2' H2' 7MG sing 21 n n O2' HO2' 7MG sing 22 n n C1' N9 7MG sing 23 n n C1' H1' 7MG sing 24 n n N9 C8 7MG sing 25 n n N9 C4 7MG sing 26 n n C8 N7 7MG sing 27 n n C8 H81 7MG sing 28 n n C8 H82 7MG sing 29 n n N7 C5 7MG sing 30 n n N7 CM7 7MG sing 31 n n C5 C6 7MG sing 32 n n C5 C4 7MG doub 33 n n C6 O6 7MG doub 34 n n C6 N1 7MG sing 35 n n N1 C2 7MG sing 36 n n N1 HN1 7MG sing 37 n n C2 N2 7MG sing 38 n n C2 N3 7MG doub 39 n n N2 HN21 7MG sing 40 n n N2 HN22 7MG sing 41 n n N3 C4 7MG sing 42 n n CM7 HM71 7MG sing 43 n n CM7 HM72 7MG sing 44 n n CM7 HM73 7MG sing 45 n n # _atom_sites.entry_id 3D45 _atom_sites.fract_transf_matrix[1][1] 0.017238 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007791 _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] 0.005655 _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 7MG A 1 651 651 7MG 7MG . D 3 GDP A 1 652 652 GDP GDP . E 2 7MG B 1 1152 1152 7MG 7MG . F 3 GDP B 1 1151 1151 GDP GDP . G 4 HOH A 1 902 4 HOH HOH . G 4 HOH A 2 903 5 HOH HOH . G 4 HOH A 3 904 6 HOH HOH . G 4 HOH A 4 905 7 HOH HOH . G 4 HOH A 5 906 11 HOH HOH . G 4 HOH A 6 907 14 HOH HOH . G 4 HOH A 7 908 15 HOH HOH . G 4 HOH A 8 909 18 HOH HOH . G 4 HOH A 9 910 22 HOH HOH . G 4 HOH A 10 911 24 HOH HOH . G 4 HOH A 11 912 26 HOH HOH . G 4 HOH A 12 913 29 HOH HOH . G 4 HOH A 13 914 30 HOH HOH . G 4 HOH A 14 915 32 HOH HOH . G 4 HOH A 15 916 37 HOH HOH . G 4 HOH A 16 917 38 HOH HOH . G 4 HOH A 17 918 39 HOH HOH . G 4 HOH A 18 919 41 HOH HOH . G 4 HOH A 19 920 42 HOH HOH . G 4 HOH A 20 921 45 HOH HOH . G 4 HOH A 21 922 46 HOH HOH . G 4 HOH A 22 923 47 HOH HOH . G 4 HOH A 23 924 53 HOH HOH . G 4 HOH A 24 925 54 HOH HOH . G 4 HOH A 25 926 55 HOH HOH . G 4 HOH A 26 927 59 HOH HOH . G 4 HOH A 27 928 68 HOH HOH . G 4 HOH A 28 929 70 HOH HOH . G 4 HOH A 29 930 71 HOH HOH . G 4 HOH A 30 931 73 HOH HOH . G 4 HOH A 31 932 75 HOH HOH . G 4 HOH A 32 933 77 HOH HOH . G 4 HOH A 33 934 79 HOH HOH . G 4 HOH A 34 935 80 HOH HOH . H 4 HOH B 1 1153 1 HOH HOH . H 4 HOH B 2 1154 2 HOH HOH . H 4 HOH B 3 1155 3 HOH HOH . H 4 HOH B 4 1156 8 HOH HOH . H 4 HOH B 5 1157 9 HOH HOH . H 4 HOH B 6 1158 10 HOH HOH . H 4 HOH B 7 1159 12 HOH HOH . H 4 HOH B 8 1160 13 HOH HOH . H 4 HOH B 9 1161 16 HOH HOH . H 4 HOH B 10 1162 17 HOH HOH . H 4 HOH B 11 1163 19 HOH HOH . H 4 HOH B 12 1164 20 HOH HOH . H 4 HOH B 13 1165 21 HOH HOH . H 4 HOH B 14 1166 23 HOH HOH . H 4 HOH B 15 1167 25 HOH HOH . H 4 HOH B 16 1168 27 HOH HOH . H 4 HOH B 17 1169 28 HOH HOH . H 4 HOH B 18 1170 31 HOH HOH . H 4 HOH B 19 1171 33 HOH HOH . H 4 HOH B 20 1172 34 HOH HOH . H 4 HOH B 21 1173 35 HOH HOH . H 4 HOH B 22 1174 36 HOH HOH . H 4 HOH B 23 1175 40 HOH HOH . H 4 HOH B 24 1176 43 HOH HOH . H 4 HOH B 25 1177 44 HOH HOH . H 4 HOH B 26 1178 48 HOH HOH . H 4 HOH B 27 1179 49 HOH HOH . H 4 HOH B 28 1180 51 HOH HOH . H 4 HOH B 29 1181 52 HOH HOH . H 4 HOH B 30 1182 56 HOH HOH . H 4 HOH B 31 1183 57 HOH HOH . H 4 HOH B 32 1184 60 HOH HOH . H 4 HOH B 33 1185 61 HOH HOH . H 4 HOH B 34 1186 62 HOH HOH . H 4 HOH B 35 1187 63 HOH HOH . H 4 HOH B 36 1188 64 HOH HOH . H 4 HOH B 37 1189 65 HOH HOH . H 4 HOH B 38 1190 66 HOH HOH . H 4 HOH B 39 1191 67 HOH HOH . H 4 HOH B 40 1192 69 HOH HOH . H 4 HOH B 41 1193 72 HOH HOH . H 4 HOH B 42 1194 74 HOH HOH . H 4 HOH B 43 1195 76 HOH HOH . H 4 HOH B 44 1196 78 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 P 7MG . . . C 2 7.027 14.583 25.219 1 56.13 ? P 7MG 651 A 1 HETATM 2 O OP1 7MG . . . C 2 6.256 14.955 26.442 1 54.54 ? OP1 7MG 651 A 1 HETATM 3 O OP2 7MG . . . C 2 8.471 14.874 25.023 1 54.77 ? OP2 7MG 651 A 1 HETATM 4 O O5' 7MG . . . C 2 6.925 13.023 25.003 1 58.63 ? O5' 7MG 651 A 1 HETATM 5 C C5' 7MG . . . C 2 7.951 12.364 25.634 1 62.57 ? C5' 7MG 651 A 1 HETATM 6 C C4' 7MG . . . C 2 7.634 10.909 25.87 1 64.81 ? C4' 7MG 651 A 1 HETATM 7 O O4' 7MG . . . C 2 8.151 10.586 27.176 1 65.74 ? O4' 7MG 651 A 1 HETATM 8 C C3' 7MG . . . C 2 6.182 10.464 25.825 1 64.4 ? C3' 7MG 651 A 1 HETATM 9 O O3' 7MG . . . C 2 6.202 9.226 25.18 1 66.47 ? O3' 7MG 651 A 1 HETATM 10 C C2' 7MG . . . C 2 5.791 10.205 27.26 1 65.2 ? C2' 7MG 651 A 1 HETATM 11 O O2' 7MG . . . C 2 5.351 8.878 27.458 1 68.05 ? O2' 7MG 651 A 1 HETATM 12 C C1' 7MG . . . C 2 7.085 10.318 28.041 1 64.74 ? C1' 7MG 651 A 1 HETATM 13 N N9 7MG . . . C 2 6.929 11.325 29.059 1 64.04 ? N9 7MG 651 A 1 HETATM 14 C C8 7MG . . . C 2 6.777 12.684 28.925 1 63.84 ? C8 7MG 651 A 1 HETATM 15 N N7 7MG . . . C 2 6.62 13.247 30.091 1 63.92 ? N7 7MG 651 A 1 HETATM 16 C C5 7MG . . . C 2 6.67 12.204 30.995 1 63.43 ? C5 7MG 651 A 1 HETATM 17 C C6 7MG . . . C 2 6.549 12.227 32.384 1 64.26 ? C6 7MG 651 A 1 HETATM 18 O O6 7MG . . . C 2 6.384 13.216 33.108 1 64.61 ? O6 7MG 651 A 1 HETATM 19 N N1 7MG . . . C 2 6.659 10.951 32.929 1 65.1 ? N1 7MG 651 A 1 HETATM 20 C C2 7MG . . . C 2 6.852 9.777 32.24 1 64.6 ? C2 7MG 651 A 1 HETATM 21 N N2 7MG . . . C 2 6.929 8.655 32.995 1 63.67 ? N2 7MG 651 A 1 HETATM 22 N N3 7MG . . . C 2 6.95 9.759 30.91 1 64.28 ? N3 7MG 651 A 1 HETATM 23 C C4 7MG . . . C 2 6.851 11.008 30.379 1 63.32 ? C4 7MG 651 A 1 HETATM 24 C CM7 7MG . . . C 2 6.507 14.671 30.429 1 62.63 ? CM7 7MG 651 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 24 #