data_4EI9 # _model_server_result.job_id iDSNf6sehkaRyI2Qttt6rw _model_server_result.datetime_utc '2024-11-26 02:13:02' _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 4ei9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 4EI9 # _exptl.entry_id 4EI9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 105.22 _cell.angle_gamma 90 _cell.entry_id 4EI9 _cell.length_a 49.501 _cell.length_b 76.443 _cell.length_c 97.628 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4EI9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C 1 1 B,D 2 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 D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 O3B GSP sing 174 n n PG S1G GSP doub 175 n n PG O2G GSP sing 176 n n PG O3G GSP sing 177 n n O3B PB GSP sing 178 n n O2G HOG2 GSP sing 179 n n O3G HOG3 GSP sing 180 n n PB O1B GSP doub 181 n n PB O2B GSP sing 182 n n PB O3A GSP sing 183 n n O2B HOB2 GSP sing 184 n n PA O1A GSP doub 185 n n PA O2A GSP sing 186 n n PA O3A GSP sing 187 n n PA O5' GSP sing 188 n n O2A HOA2 GSP sing 189 n n O5' C5' GSP sing 190 n n C5' C4' GSP sing 191 n n C5' "H5'1" GSP sing 192 n n C5' "H5'2" GSP sing 193 n n C4' O4' GSP sing 194 n n C4' C3' GSP sing 195 n n C4' H4' GSP sing 196 n n O4' C1' GSP sing 197 n n C3' O3' GSP sing 198 n n C3' C2' GSP sing 199 n n C3' H3' GSP sing 200 n n O3' HO3' GSP sing 201 n n C2' O2' GSP sing 202 n n C2' C1' GSP sing 203 n n C2' H2' GSP sing 204 n n O2' HO2' GSP sing 205 n n C1' N9 GSP sing 206 n n C1' H1' GSP sing 207 n n N9 C8 GSP sing 208 n y N9 C4 GSP sing 209 n y C8 N7 GSP doub 210 n y C8 H8 GSP sing 211 n n N7 C5 GSP sing 212 n y C5 C6 GSP sing 213 n n C5 C4 GSP doub 214 n y C6 O6 GSP doub 215 n n C6 N1 GSP sing 216 n n N1 C2 GSP sing 217 n n N1 HN1 GSP sing 218 n n C2 N2 GSP sing 219 n n C2 N3 GSP doub 220 n n N2 HN21 GSP sing 221 n n N2 HN22 GSP sing 222 n n N3 C4 GSP sing 223 n n # _atom_sites.entry_id 4EI9 _atom_sites.fract_transf_matrix[1][1] 0.020202 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005496 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013082 _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] 0.010615 _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 GDP A 1 500 500 GDP GDP . D 3 GSP B 1 500 500 GSP GSP . # 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 GSP . . . D 3 3.884 10.65 -101.323 1 142.75 ? PG GSP 500 B 1 HETATM 2 O O3B GSP . . . D 3 3.685 9.48 -100.174 1 130.7 ? O3B GSP 500 B 1 HETATM 3 S S1G GSP . . . D 3 4.531 9.519 -102.662 1 142.77 ? S1G GSP 500 B 1 HETATM 4 O O2G GSP . . . D 3 2.493 11.183 -101.437 1 131.02 ? O2G GSP 500 B 1 HETATM 5 O O3G GSP . . . D 3 5.059 11.542 -101.057 1 130.94 ? O3G GSP 500 B 1 HETATM 6 P PB GSP . . . D 3 3.13 9.611 -98.603 1 116.69 ? PB GSP 500 B 1 HETATM 7 O O1B GSP . . . D 3 2.864 11.02 -98.516 1 108.46 ? O1B GSP 500 B 1 HETATM 8 O O2B GSP . . . D 3 1.897 8.815 -98.277 1 94.49 ? O2B GSP 500 B 1 HETATM 9 P PA GSP . . . D 3 4.839 7.615 -97.57 1 96.33 ? PA GSP 500 B 1 HETATM 10 O O1A GSP . . . D 3 3.761 6.832 -96.914 1 92.05 ? O1A GSP 500 B 1 HETATM 11 O O2A GSP . . . D 3 5.449 7.229 -98.893 1 95.09 ? O2A GSP 500 B 1 HETATM 12 O O3A GSP . . . D 3 4.334 9.1 -97.667 1 104.33 ? O3A GSP 500 B 1 HETATM 13 O O5' GSP . . . D 3 6.077 7.688 -96.473 1 97.99 ? O5' GSP 500 B 1 HETATM 14 C C5' GSP . . . D 3 6.561 8.894 -95.774 1 87.42 ? C5' GSP 500 B 1 HETATM 15 C C4' GSP . . . D 3 7.706 8.463 -94.869 1 96.98 ? C4' GSP 500 B 1 HETATM 16 O O4' GSP . . . D 3 7.336 7.289 -94.03 1 99.09 ? O4' GSP 500 B 1 HETATM 17 C C3' GSP . . . D 3 9.027 8.037 -95.616 1 96.69 ? C3' GSP 500 B 1 HETATM 18 O O3' GSP . . . D 3 10.044 9.043 -95.294 1 107.52 ? O3' GSP 500 B 1 HETATM 19 C C2' GSP . . . D 3 9.416 6.584 -95.103 1 98.28 ? C2' GSP 500 B 1 HETATM 20 O O2' GSP . . . D 3 10.746 6.529 -94.478 1 86.2 ? O2' GSP 500 B 1 HETATM 21 C C1' GSP . . . D 3 8.252 6.153 -94.118 1 94.14 ? C1' GSP 500 B 1 HETATM 22 N N9 GSP . . . D 3 7.369 5.003 -94.554 1 90.53 ? N9 GSP 500 B 1 HETATM 23 C C8 GSP . . . D 3 6.56 4.769 -95.671 1 93.97 ? C8 GSP 500 B 1 HETATM 24 N N7 GSP . . . D 3 5.923 3.631 -95.717 1 94.14 ? N7 GSP 500 B 1 HETATM 25 C C5 GSP . . . D 3 6.333 3.03 -94.524 1 91.83 ? C5 GSP 500 B 1 HETATM 26 C C6 GSP . . . D 3 5.964 1.7 -93.965 1 104.43 ? C6 GSP 500 B 1 HETATM 27 O O6 GSP . . . D 3 5.189 0.936 -94.562 1 121.5 ? O6 GSP 500 B 1 HETATM 28 N N1 GSP . . . D 3 6.624 1.463 -92.684 1 100.78 ? N1 GSP 500 B 1 HETATM 29 C C2 GSP . . . D 3 7.52 2.359 -92.005 1 89.62 ? C2 GSP 500 B 1 HETATM 30 N N2 GSP . . . D 3 8.061 2.038 -90.846 1 86.73 ? N2 GSP 500 B 1 HETATM 31 N N3 GSP . . . D 3 7.847 3.593 -92.549 1 93.06 ? N3 GSP 500 B 1 HETATM 32 C C4 GSP . . . D 3 7.225 3.868 -93.802 1 87.77 ? C4 GSP 500 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #