data_3D45 # _model_server_result.job_id WFIeZWQ12Hxpdyb-cbK0zg _model_server_result.datetime_utc '2024-11-20 07:34:25' _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":"D","auth_seq_id":652}' # _entry.id 3D45 # _exptl.entry_id 3D45 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 ? 3 D N N ? 3 F N N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _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 PB O1B GDP doub 128 n n PB O2B GDP sing 129 n n PB O3B GDP sing 130 n n PB O3A GDP sing 131 n n O2B HOB2 GDP sing 132 n n O3B HOB3 GDP sing 133 n n O3A PA GDP sing 134 n n PA O1A GDP doub 135 n n PA O2A GDP sing 136 n n PA O5' GDP sing 137 n n O2A HOA2 GDP sing 138 n n O5' C5' GDP sing 139 n n C5' C4' GDP sing 140 n n C5' H5' GDP sing 141 n n C5' "H5''" GDP sing 142 n n C4' O4' GDP sing 143 n n C4' C3' GDP sing 144 n n C4' H4' GDP sing 145 n n O4' C1' GDP sing 146 n n C3' O3' GDP sing 147 n n C3' C2' GDP sing 148 n n C3' H3' GDP sing 149 n n O3' HO3' GDP sing 150 n n C2' O2' GDP sing 151 n n C2' C1' GDP sing 152 n n C2' H2' GDP sing 153 n n O2' HO2' GDP sing 154 n n C1' N9 GDP sing 155 n n C1' H1' GDP sing 156 n n N9 C8 GDP sing 157 n y N9 C4 GDP sing 158 n y C8 N7 GDP doub 159 n y C8 H8 GDP sing 160 n n N7 C5 GDP sing 161 n y C5 C6 GDP sing 162 n n C5 C4 GDP doub 163 n y C6 O6 GDP doub 164 n n C6 N1 GDP sing 165 n n N1 C2 GDP sing 166 n n N1 HN1 GDP sing 167 n n C2 N2 GDP sing 168 n n C2 N3 GDP doub 169 n n N2 HN21 GDP sing 170 n n N2 HN22 GDP sing 171 n n N3 C4 GDP sing 172 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 PB GDP . . . D 3 5.027 14.198 23.058 1 63.92 ? PB GDP 652 A 1 HETATM 2 O O1B GDP . . . D 3 5.253 12.846 22.439 1 65.42 ? O1B GDP 652 A 1 HETATM 3 O O2B GDP . . . D 3 4.551 14.02 24.477 1 64.06 ? O2B GDP 652 A 1 HETATM 4 O O3B GDP . . . D 3 6.33 14.956 22.939 1 64.38 ? O3B GDP 652 A 1 HETATM 5 O O3A GDP . . . D 3 3.847 14.992 22.325 1 63 ? O3A GDP 652 A 1 HETATM 6 P PA GDP . . . D 3 4.073 16.415 21.616 1 62.12 ? PA GDP 652 A 1 HETATM 7 O O1A GDP . . . D 3 2.699 17.028 21.349 1 63.25 ? O1A GDP 652 A 1 HETATM 8 O O2A GDP . . . D 3 4.994 17.353 22.366 1 60.12 ? O2A GDP 652 A 1 HETATM 9 O O5' GDP . . . D 3 4.703 15.903 20.242 1 60.38 ? O5' GDP 652 A 1 HETATM 10 C C5' GDP . . . D 3 3.966 14.908 19.541 1 59.99 ? C5' GDP 652 A 1 HETATM 11 C C4' GDP . . . D 3 4.175 15.05 18.052 1 59.7 ? C4' GDP 652 A 1 HETATM 12 O O4' GDP . . . D 3 5.467 14.558 17.714 1 61.51 ? O4' GDP 652 A 1 HETATM 13 C C3' GDP . . . D 3 3.189 14.181 17.319 1 58.95 ? C3' GDP 652 A 1 HETATM 14 O O3' GDP . . . D 3 2.238 15.064 16.737 1 60.48 ? O3' GDP 652 A 1 HETATM 15 C C2' GDP . . . D 3 3.976 13.411 16.28 1 58.46 ? C2' GDP 652 A 1 HETATM 16 O O2' GDP . . . D 3 3.628 13.81 14.96 1 57.22 ? O2' GDP 652 A 1 HETATM 17 C C1' GDP . . . D 3 5.42 13.798 16.511 1 60.51 ? C1' GDP 652 A 1 HETATM 18 N N9 GDP . . . D 3 6.306 12.607 16.602 1 61.43 ? N9 GDP 652 A 1 HETATM 19 C C8 GDP . . . D 3 5.947 11.319 16.819 1 61.38 ? C8 GDP 652 A 1 HETATM 20 N N7 GDP . . . D 3 7.024 10.487 16.806 1 60.39 ? N7 GDP 652 A 1 HETATM 21 C C5 GDP . . . D 3 8.102 11.253 16.586 1 60.92 ? C5 GDP 652 A 1 HETATM 22 C C6 GDP . . . D 3 9.558 11.034 16.455 1 60.93 ? C6 GDP 652 A 1 HETATM 23 O O6 GDP . . . D 3 10.045 9.895 16.559 1 61.8 ? O6 GDP 652 A 1 HETATM 24 N N1 GDP . . . D 3 10.355 12.072 16.22 1 60.79 ? N1 GDP 652 A 1 HETATM 25 C C2 GDP . . . D 3 9.862 13.308 16.111 1 60.88 ? C2 GDP 652 A 1 HETATM 26 N N2 GDP . . . D 3 10.743 14.309 15.881 1 61.45 ? N2 GDP 652 A 1 HETATM 27 N N3 GDP . . . D 3 8.539 13.598 16.213 1 61.03 ? N3 GDP 652 A 1 HETATM 28 C C4 GDP . . . D 3 7.63 12.635 16.449 1 61.22 ? C4 GDP 652 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #