data_5EUQ # _model_server_result.job_id '_aNdRW0gkvrFVo5Bg89OAg' _model_server_result.datetime_utc '2024-11-08 18:21:36' _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 5euq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5EUQ # _exptl.entry_id 5EUQ _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 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 90 _cell.entry_id 5EUQ _cell.length_a 48.9 _cell.length_b 103.49 _cell.length_c 188.94 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EUQ _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 146 n n PB O2B GDP sing 147 n n PB O3B GDP sing 148 n n PB O3A GDP sing 149 n n O2B HOB2 GDP sing 150 n n O3B HOB3 GDP sing 151 n n O3A PA GDP sing 152 n n PA O1A GDP doub 153 n n PA O2A GDP sing 154 n n PA O5' GDP sing 155 n n O2A HOA2 GDP sing 156 n n O5' C5' GDP sing 157 n n C5' C4' GDP sing 158 n n C5' H5' GDP sing 159 n n C5' "H5''" GDP sing 160 n n C4' O4' GDP sing 161 n n C4' C3' GDP sing 162 n n C4' H4' GDP sing 163 n n O4' C1' GDP sing 164 n n C3' O3' GDP sing 165 n n C3' C2' GDP sing 166 n n C3' H3' GDP sing 167 n n O3' HO3' GDP sing 168 n n C2' O2' GDP sing 169 n n C2' C1' GDP sing 170 n n C2' H2' GDP sing 171 n n O2' HO2' GDP sing 172 n n C1' N9 GDP sing 173 n n C1' H1' GDP sing 174 n n N9 C8 GDP sing 175 n y N9 C4 GDP sing 176 n y C8 N7 GDP doub 177 n y C8 H8 GDP sing 178 n n N7 C5 GDP sing 179 n y C5 C6 GDP sing 180 n n C5 C4 GDP doub 181 n y C6 O6 GDP doub 182 n n C6 N1 GDP sing 183 n n N1 C2 GDP sing 184 n n N1 HN1 GDP sing 185 n n C2 N2 GDP sing 186 n n C2 N3 GDP doub 187 n n N2 HN21 GDP sing 188 n n N2 HN22 GDP sing 189 n n N3 C4 GDP sing 190 n n # _atom_sites.entry_id 5EUQ _atom_sites.fract_transf_matrix[1][1] 0.02045 _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] 0.009663 _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] 0.005293 _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 3 GDP B 1 301 1174 GDP GDP . D 4 SO4 E 1 1001 1001 SO4 SO4 . E 4 SO4 E 1 1002 1002 SO4 SO4 . F 5 5S8 E 1 1003 2001 5S8 DRG . # 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 . . . C 3 -235.703 211.349 362.207 1 98.4 ? PB GDP 301 B 1 HETATM 2 O O1B GDP . . . C 3 -235.315 210.543 360.991 1 98.4 -1 O1B GDP 301 B 1 HETATM 3 O O2B GDP . . . C 3 -236.142 210.398 363.291 1 98.4 ? O2B GDP 301 B 1 HETATM 4 O O3B GDP . . . C 3 -236.849 212.274 361.868 1 98.4 ? O3B GDP 301 B 1 HETATM 5 O O3A GDP . . . C 3 -234.429 212.201 362.711 1 98.4 ? O3A GDP 301 B 1 HETATM 6 P PA GDP . . . C 3 -234.592 213.434 363.736 1 98.4 ? PA GDP 301 B 1 HETATM 7 O O1A GDP . . . C 3 -234.306 214.74 363.037 1 98.4 -1 O1A GDP 301 B 1 HETATM 8 O O2A GDP . . . C 3 -235.974 213.446 364.35 1 98.4 ? O2A GDP 301 B 1 HETATM 9 O O5' GDP . . . C 3 -233.483 213.164 364.871 1 98.4 ? O5' GDP 301 B 1 HETATM 10 C C5' GDP . . . C 3 -233.911 213.068 366.229 1 98.4 ? C5' GDP 301 B 1 HETATM 11 C C4' GDP . . . C 3 -232.926 213.783 367.147 1 98.4 ? C4' GDP 301 B 1 HETATM 12 O O4' GDP . . . C 3 -231.654 213.128 367.144 1 98.4 ? O4' GDP 301 B 1 HETATM 13 C C3' GDP . . . C 3 -232.7 215.225 366.699 1 98.4 ? C3' GDP 301 B 1 HETATM 14 O O3' GDP . . . C 3 -233.282 216.13 367.643 1 98.4 ? O3' GDP 301 B 1 HETATM 15 C C2' GDP . . . C 3 -231.194 215.403 366.652 1 98.4 ? C2' GDP 301 B 1 HETATM 16 O O2' GDP . . . C 3 -230.762 216.56 367.382 1 98.4 ? O2' GDP 301 B 1 HETATM 17 C C1' GDP . . . C 3 -230.64 214.127 367.269 1 98.4 ? C1' GDP 301 B 1 HETATM 18 N N9 GDP . . . C 3 -229.408 213.722 366.556 1 98.4 ? N9 GDP 301 B 1 HETATM 19 C C8 GDP . . . C 3 -229.311 213.355 365.266 1 98.4 ? C8 GDP 301 B 1 HETATM 20 N N7 GDP . . . C 3 -228.029 213.045 364.939 1 98.4 ? N7 GDP 301 B 1 HETATM 21 C C5 GDP . . . C 3 -227.284 213.213 366.047 1 98.4 ? C5 GDP 301 B 1 HETATM 22 C C6 GDP . . . C 3 -225.859 213.062 366.414 1 98.4 ? C6 GDP 301 B 1 HETATM 23 O O6 GDP . . . C 3 -225.016 212.689 365.573 1 98.4 ? O6 GDP 301 B 1 HETATM 24 N N1 GDP . . . C 3 -225.503 213.338 367.677 1 98.4 ? N1 GDP 301 B 1 HETATM 25 C C2 GDP . . . C 3 -226.389 213.743 368.611 1 98.4 ? C2 GDP 301 B 1 HETATM 26 N N2 GDP . . . C 3 -225.946 214.002 369.866 1 98.4 ? N2 GDP 301 B 1 HETATM 27 N N3 GDP . . . C 3 -227.711 213.904 368.347 1 98.4 ? N3 GDP 301 B 1 HETATM 28 C C4 GDP . . . C 3 -228.2 213.657 367.109 1 98.4 ? C4 GDP 301 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #