data_4DVG # _model_server_result.job_id jijy9uu7mbx36H0zAvAhXg _model_server_result.datetime_utc '2024-11-05 00:31:03' _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 4dvg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":200}' # _entry.id 4DVG # _exptl.entry_id 4DVG _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 90 _cell.angle_gamma 120 _cell.entry_id 4DVG _cell.length_a 138.564 _cell.length_b 138.564 _cell.length_c 57.765 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DVG _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 B C GLU 20 B GLU 85 1_555 B N MSE 21 B MSE 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 B C MSE 21 B MSE 86 1_555 B N LYS 22 B LYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 B C ASP 80 B ASP 145 1_555 B N MSE 81 B MSE 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 B C MSE 81 B MSE 146 1_555 B N ASP 82 B ASP 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale5 B C GLU 86 B GLU 151 1_555 B N MSE 87 B MSE 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 B C MSE 87 B MSE 152 1_555 B N VAL 88 B VAL 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 B C LEU 111 B LEU 176 1_555 B N MSE 112 B MSE 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale8 B C MSE 112 B MSE 177 1_555 B N ALA 113 B ALA 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 B C GLY 164 B GLY 229 1_555 B N MSE 165 B MSE 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 B C MSE 165 B MSE 230 1_555 B N ASN 166 B ASN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale11 B C SER 187 B SER 252 1_555 B N MSE 188 B MSE 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale12 B C MSE 188 B MSE 253 1_555 B N VAL 189 B VAL 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale13 B C VAL 205 B VAL 270 1_555 B N MSE 206 B MSE 271 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale14 B C MSE 206 B MSE 271 1_555 B N ASN 207 B ASN 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale15 B C ASP 218 B ASP 283 1_555 B N MSE 219 B MSE 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale16 B C MSE 219 B MSE 284 1_555 B N LYS 220 B LYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale17 B C ARG 257 B ARG 322 1_555 B N MSE 258 B MSE 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale18 B C MSE 258 B MSE 323 1_555 B N ASP 259 B ASP 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale19 B C ASN 275 B ASN 340 1_555 B N MSE 276 B MSE 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale20 B C MSE 276 B MSE 341 1_555 B N LYS 277 B LYS 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale21 B C TRP 281 B TRP 346 1_555 B N MSE 282 B MSE 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale22 B C MSE 282 B MSE 347 1_555 B N LYS 283 B LYS 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 C O2B GSP . A GSP 200 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? metalc ? metalc2 C O2G GSP . A GSP 200 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc3 A OG1 THR 54 A THR 52 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc4 A OG1 THR 36 A THR 34 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? # _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 ? # _atom_sites.entry_id 4DVG _atom_sites.fract_transf_matrix[1][1] 0.007217 _atom_sites.fract_transf_matrix[1][2] 0.004167 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008333 _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] 0.017312 _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 GSP A 1 200 200 GSP GSP . D 4 MG A 1 201 201 MG MG . E 5 HOH A 1 301 3 HOH HOH . E 5 HOH A 2 302 4 HOH HOH . F 5 HOH B 1 501 1 HOH HOH . F 5 HOH B 2 502 2 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 PG GSP . . . C 3 43.424 52.483 10.086 1 51.85 ? PG GSP 200 A 1 HETATM 2 O O3B GSP . . . C 3 42.726 53.921 9.849 0.77 46.52 ? O3B GSP 200 A 1 HETATM 3 S S1G GSP . . . C 3 42.773 51.335 8.988 1 62 ? S1G GSP 200 A 1 HETATM 4 O O2G GSP . . . C 3 44.947 52.624 9.867 1 56.94 ? O2G GSP 200 A 1 HETATM 5 O O3G GSP . . . C 3 43.158 52.049 11.539 1 49.79 ? O3G GSP 200 A 1 HETATM 6 P PB GSP . . . C 3 43.217 55.284 10.56 1 52.18 ? PB GSP 200 A 1 HETATM 7 O O1B GSP . . . C 3 42.525 55.506 11.837 1 56.54 ? O1B GSP 200 A 1 HETATM 8 O O2B GSP . . . C 3 44.688 55.346 10.763 1 65.71 ? O2B GSP 200 A 1 HETATM 9 P PA GSP . . . C 3 43.774 57.445 8.85 1 56.81 ? PA GSP 200 A 1 HETATM 10 O O1A GSP . . . C 3 44.446 58.22 9.916 1 48.55 ? O1A GSP 200 A 1 HETATM 11 O O2A GSP . . . C 3 44.766 56.817 7.956 1 58.61 ? O2A GSP 200 A 1 HETATM 12 O O3A GSP . . . C 3 42.733 56.383 9.501 1 42.12 ? O3A GSP 200 A 1 HETATM 13 O O5' GSP . . . C 3 42.703 58.317 8.049 1 45.17 ? O5' GSP 200 A 1 HETATM 14 C C5' GSP . . . C 3 41.58 57.653 7.502 1 43.83 ? C5' GSP 200 A 1 HETATM 15 C C4' GSP . . . C 3 41.094 58.48 6.32 1 60.11 ? C4' GSP 200 A 1 HETATM 16 O O4' GSP . . . C 3 40.312 59.562 6.806 1 62.03 ? O4' GSP 200 A 1 HETATM 17 C C3' GSP . . . C 3 42.259 59.069 5.53 1 67.14 ? C3' GSP 200 A 1 HETATM 18 O O3' GSP . . . C 3 42.046 58.88 4.153 1 72.38 ? O3' GSP 200 A 1 HETATM 19 C C2' GSP . . . C 3 42.235 60.55 5.828 1 68.28 ? C2' GSP 200 A 1 HETATM 20 O O2' GSP . . . C 3 42.276 61.283 4.632 0.64 77.91 ? O2' GSP 200 A 1 HETATM 21 C C1' GSP . . . C 3 40.892 60.811 6.478 1 61.75 ? C1' GSP 200 A 1 HETATM 22 N N9 GSP . . . C 3 41.098 61.645 7.678 1 53.25 ? N9 GSP 200 A 1 HETATM 23 C C8 GSP . . . C 3 41.926 61.384 8.726 0 52.68 ? C8 GSP 200 A 1 HETATM 24 N N7 GSP . . . C 3 41.801 62.419 9.579 1 52.47 ? N7 GSP 200 A 1 HETATM 25 C C5 GSP . . . C 3 40.929 63.324 9.111 0 54.42 ? C5 GSP 200 A 1 HETATM 26 C C6 GSP . . . C 3 40.45 64.536 9.577 1 58.65 ? C6 GSP 200 A 1 HETATM 27 O O6 GSP . . . C 3 40.825 64.992 10.655 0.77 67.16 ? O6 GSP 200 A 1 HETATM 28 N N1 GSP . . . C 3 39.538 65.24 8.83 1 53.85 ? N1 GSP 200 A 1 HETATM 29 C C2 GSP . . . C 3 39.096 64.741 7.624 1 56.11 ? C2 GSP 200 A 1 HETATM 30 N N2 GSP . . . C 3 38.195 65.406 6.883 1 59.51 ? N2 GSP 200 A 1 HETATM 31 N N3 GSP . . . C 3 39.584 63.535 7.185 0.88 53.48 ? N3 GSP 200 A 1 HETATM 32 C C4 GSP . . . C 3 40.481 62.838 7.912 1 52.35 ? C4 GSP 200 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #