data_8VOF # _model_server_result.job_id 56rb70txh53xrszmT1ubSw _model_server_result.datetime_utc '2024-10-17 16:20:01' _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 8vof # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 8VOF # _exptl.entry_id 8VOF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 8VOF _cell.length_a 48.57 _cell.length_b 105.224 _cell.length_c 186.423 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VOF _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 5 _struct_asym.id E _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 141 n n PB O2B GDP sing 142 n n PB O3B GDP sing 143 n n PB O3A GDP sing 144 n n O2B HOB2 GDP sing 145 n n O3B HOB3 GDP sing 146 n n O3A PA GDP sing 147 n n PA O1A GDP doub 148 n n PA O2A GDP sing 149 n n PA O5' GDP sing 150 n n O2A HOA2 GDP sing 151 n n O5' C5' GDP sing 152 n n C5' C4' GDP sing 153 n n C5' H5' GDP sing 154 n n C5' "H5''" GDP sing 155 n n C4' O4' GDP sing 156 n n C4' C3' GDP sing 157 n n C4' H4' GDP sing 158 n n O4' C1' GDP sing 159 n n C3' O3' GDP sing 160 n n C3' C2' GDP sing 161 n n C3' H3' GDP sing 162 n n O3' HO3' GDP sing 163 n n C2' O2' GDP sing 164 n n C2' C1' GDP sing 165 n n C2' H2' GDP sing 166 n n O2' HO2' GDP sing 167 n n C1' N9 GDP sing 168 n n C1' H1' GDP sing 169 n n N9 C8 GDP sing 170 n y N9 C4 GDP sing 171 n y C8 N7 GDP doub 172 n y C8 H8 GDP sing 173 n n N7 C5 GDP sing 174 n y C5 C6 GDP sing 175 n n C5 C4 GDP doub 176 n y C6 O6 GDP doub 177 n n C6 N1 GDP sing 178 n n N1 C2 GDP sing 179 n n N1 HN1 GDP sing 180 n n C2 N2 GDP sing 181 n n C2 N3 GDP doub 182 n n N2 HN21 GDP sing 183 n n N2 HN22 GDP sing 184 n n N3 C4 GDP sing 185 n n # _atom_sites.entry_id 8VOF _atom_sites.fract_transf_matrix[1][1] 0.020589 _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] 0.009504 _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] 0.005364 _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 A1ADE A 1 1101 1101 A1ADE LI1 . D 4 SO4 A 1 1102 1 SO4 SO4 . E 5 GDP B 1 301 201 GDP GDP . F 6 HOH A 1 1201 7 HOH HOH . F 6 HOH A 2 1202 4 HOH HOH . F 6 HOH A 3 1203 1 HOH HOH . F 6 HOH A 4 1204 5 HOH HOH . F 6 HOH A 5 1205 3 HOH HOH . F 6 HOH A 6 1206 8 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 . . . E 5 -10.407 -5.702 -14.469 1 99.01 ? PB GDP 301 B 1 HETATM 2 O O1B GDP . . . E 5 -9.005 -5.17 -14.276 1 76.88 ? O1B GDP 301 B 1 HETATM 3 O O2B GDP . . . E 5 -11.383 -4.548 -14.494 1 85.34 ? O2B GDP 301 B 1 HETATM 4 O O3B GDP . . . E 5 -10.471 -6.478 -15.76 1 103.31 ? O3B GDP 301 B 1 HETATM 5 O O3A GDP . . . E 5 -10.793 -6.658 -13.235 1 99.6 ? O3A GDP 301 B 1 HETATM 6 P PA GDP . . . E 5 -11.497 -8.088 -13.45 1 93.12 ? PA GDP 301 B 1 HETATM 7 O O1A GDP . . . E 5 -10.542 -9.082 -14.067 1 103.19 ? O1A GDP 301 B 1 HETATM 8 O O2A GDP . . . E 5 -12.752 -7.95 -14.278 1 91.47 ? O2A GDP 301 B 1 HETATM 9 O O5' GDP . . . E 5 -11.857 -8.494 -11.937 1 115.16 ? O5' GDP 301 B 1 HETATM 10 C C5' GDP . . . E 5 -12.732 -7.641 -11.205 1 99.41 ? C5' GDP 301 B 1 HETATM 11 C C4' GDP . . . E 5 -13.266 -8.37 -9.983 1 78.14 ? C4' GDP 301 B 1 HETATM 12 O O4' GDP . . . E 5 -14.589 -7.893 -9.757 1 75.27 ? O4' GDP 301 B 1 HETATM 13 C C3' GDP . . . E 5 -13.375 -9.856 -10.249 1 89.12 ? C3' GDP 301 B 1 HETATM 14 O O3' GDP . . . E 5 -13.186 -10.578 -9.029 1 85.11 ? O3' GDP 301 B 1 HETATM 15 C C2' GDP . . . E 5 -14.792 -10.033 -10.742 1 87.47 ? C2' GDP 301 B 1 HETATM 16 O O2' GDP . . . E 5 -15.322 -11.302 -10.362 1 98.09 ? O2' GDP 301 B 1 HETATM 17 C C1' GDP . . . E 5 -15.55 -8.902 -10.069 1 65.35 ? C1' GDP 301 B 1 HETATM 18 N N9 GDP . . . E 5 -16.549 -8.332 -10.988 1 79.12 ? N9 GDP 301 B 1 HETATM 19 C C8 GDP . . . E 5 -16.366 -8.05 -12.293 1 101.79 ? C8 GDP 301 B 1 HETATM 20 N N7 GDP . . . E 5 -17.493 -7.524 -12.834 1 102.49 ? N7 GDP 301 B 1 HETATM 21 C C5 GDP . . . E 5 -18.418 -7.452 -11.852 1 90.68 ? C5 GDP 301 B 1 HETATM 22 C C6 GDP . . . E 5 -19.823 -6.998 -11.718 1 94.35 ? C6 GDP 301 B 1 HETATM 23 O O6 GDP . . . E 5 -20.455 -6.53 -12.687 1 114.73 ? O6 GDP 301 B 1 HETATM 24 N N1 GDP . . . E 5 -20.407 -7.101 -10.515 1 99.83 ? N1 GDP 301 B 1 HETATM 25 C C2 GDP . . . E 5 -19.766 -7.598 -9.443 1 106.59 ? C2 GDP 301 B 1 HETATM 26 N N2 GDP . . . E 5 -20.418 -7.673 -8.258 1 102.77 ? N2 GDP 301 B 1 HETATM 27 N N3 GDP . . . E 5 -18.484 -8.032 -9.49 1 91.36 ? N3 GDP 301 B 1 HETATM 28 C C4 GDP . . . E 5 -17.783 -7.981 -10.645 1 81.02 ? C4 GDP 301 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 443 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 28 #