data_8YAJ # _model_server_result.job_id ws_Q3OH7uHIv9aDK0QLrNQ _model_server_result.datetime_utc '2024-12-01 01:27:31' _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 8yaj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 8YAJ # _exptl.entry_id 8YAJ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 8YAJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YAJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 J N N # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G GTP doub 181 n n PG O2G GTP sing 182 n n PG O3G GTP sing 183 n n PG O3B GTP sing 184 n n O2G HOG2 GTP sing 185 n n O3G HOG3 GTP sing 186 n n O3B PB GTP sing 187 n n PB O1B GTP doub 188 n n PB O2B GTP sing 189 n n PB O3A GTP sing 190 n n O2B HOB2 GTP sing 191 n n O3A PA GTP sing 192 n n PA O1A GTP doub 193 n n PA O2A GTP sing 194 n n PA O5' GTP sing 195 n n O2A HOA2 GTP sing 196 n n O5' C5' GTP sing 197 n n C5' C4' GTP sing 198 n n C5' H5' GTP sing 199 n n C5' "H5''" GTP sing 200 n n C4' O4' GTP sing 201 n n C4' C3' GTP sing 202 n n C4' H4' GTP sing 203 n n O4' C1' GTP sing 204 n n C3' O3' GTP sing 205 n n C3' C2' GTP sing 206 n n C3' H3' GTP sing 207 n n O3' HO3' GTP sing 208 n n C2' O2' GTP sing 209 n n C2' C1' GTP sing 210 n n C2' H2' GTP sing 211 n n O2' HO2' GTP sing 212 n n C1' N9 GTP sing 213 n n C1' H1' GTP sing 214 n n N9 C8 GTP sing 215 n y N9 C4 GTP sing 216 n y C8 N7 GTP doub 217 n y C8 H8 GTP sing 218 n n N7 C5 GTP sing 219 n y C5 C6 GTP sing 220 n n C5 C4 GTP doub 221 n y C6 O6 GTP doub 222 n n C6 N1 GTP sing 223 n n N1 C2 GTP sing 224 n n N1 HN1 GTP sing 225 n n C2 N2 GTP sing 226 n n C2 N3 GTP doub 227 n n N2 HN21 GTP sing 228 n n N2 HN22 GTP sing 229 n n N3 C4 GTP sing 230 n n # _atom_sites.entry_id 8YAJ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 4 GTP B 1 501 501 GTP GTP . H 5 PIN C 1 301 201 PIN PIN . I 6 G2P D 1 501 501 G2P G2P . J 4 GTP E 1 501 501 GTP GTP . K 6 G2P F 1 501 501 G2P G2P . # 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 PG GTP . . . J 4 135.982 238.965 188.877 1 77.34 ? PG GTP 501 E 1 HETATM 2 O O1G GTP . . . J 4 134.765 239.609 188.231 1 77.34 ? O1G GTP 501 E 1 HETATM 3 O O2G GTP . . . J 4 137.303 239.408 188.275 1 77.34 ? O2G GTP 501 E 1 HETATM 4 O O3G GTP . . . J 4 135.871 237.473 189.088 1 77.34 ? O3G GTP 501 E 1 HETATM 5 O O3B GTP . . . J 4 135.934 239.692 190.439 1 77.34 ? O3B GTP 501 E 1 HETATM 6 P PB GTP . . . J 4 137.08 239.975 191.445 1 77.34 ? PB GTP 501 E 1 HETATM 7 O O1B GTP . . . J 4 136.639 240.144 192.869 1 77.34 ? O1B GTP 501 E 1 HETATM 8 O O2B GTP . . . J 4 138.408 239.34 191.163 1 77.34 ? O2B GTP 501 E 1 HETATM 9 O O3A GTP . . . J 4 137.499 241.638 191.115 1 77.34 ? O3A GTP 501 E 1 HETATM 10 P PA GTP . . . J 4 138.69 242.426 191.675 1 77.34 ? PA GTP 501 E 1 HETATM 11 O O1A GTP . . . J 4 139.387 241.962 192.921 1 77.34 ? O1A GTP 501 E 1 HETATM 12 O O2A GTP . . . J 4 139.477 243.268 190.714 1 77.34 ? O2A GTP 501 E 1 HETATM 13 O O5' GTP . . . J 4 137.811 243.805 192.504 1 77.34 ? O5' GTP 501 E 1 HETATM 14 C C5' GTP . . . J 4 137.936 245.021 191.977 1 77.34 ? C5' GTP 501 E 1 HETATM 15 C C4' GTP . . . J 4 138.807 245.864 192.978 1 77.34 ? C4' GTP 501 E 1 HETATM 16 O O4' GTP . . . J 4 139.819 245.038 193.529 1 77.34 ? O4' GTP 501 E 1 HETATM 17 C C3' GTP . . . J 4 139.555 247.01 192.25 1 77.34 ? C3' GTP 501 E 1 HETATM 18 O O3' GTP . . . J 4 139.13 248.204 192.828 1 77.34 ? O3' GTP 501 E 1 HETATM 19 C C2' GTP . . . J 4 141.041 246.751 192.574 1 77.34 ? C2' GTP 501 E 1 HETATM 20 O O2' GTP . . . J 4 141.743 247.898 192.92 1 77.34 ? O2' GTP 501 E 1 HETATM 21 C C1' GTP . . . J 4 140.882 245.881 193.849 1 77.34 ? C1' GTP 501 E 1 HETATM 22 N N9 GTP . . . J 4 142.081 245.045 194.05 1 77.34 ? N9 GTP 501 E 1 HETATM 23 C C8 GTP . . . J 4 142.557 243.99 193.26 1 77.34 ? C8 GTP 501 E 1 HETATM 24 N N7 GTP . . . J 4 143.683 243.462 193.755 1 77.34 ? N7 GTP 501 E 1 HETATM 25 C C5 GTP . . . J 4 143.942 244.205 194.906 1 77.34 ? C5 GTP 501 E 1 HETATM 26 C C6 GTP . . . J 4 145.027 244.047 195.801 1 77.34 ? C6 GTP 501 E 1 HETATM 27 O O6 GTP . . . J 4 145.963 243.255 195.788 1 77.34 ? O6 GTP 501 E 1 HETATM 28 N N1 GTP . . . J 4 144.988 244.978 196.876 1 77.34 ? N1 GTP 501 E 1 HETATM 29 C C2 GTP . . . J 4 143.963 245.925 196.982 1 77.34 ? C2 GTP 501 E 1 HETATM 30 N N2 GTP . . . J 4 144.014 246.788 198.065 1 77.34 ? N2 GTP 501 E 1 HETATM 31 N N3 GTP . . . J 4 142.925 246.095 196.149 1 77.34 ? N3 GTP 501 E 1 HETATM 32 C C4 GTP . . . J 4 142.953 245.194 195.099 1 77.34 ? C4 GTP 501 E 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #