data_6DPW # _model_server_result.job_id T6c2pT9YgtcCarKEqjkGzQ _model_server_result.datetime_utc '2025-03-04 16:24:57' _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 6dpw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":501}' # _entry.id 6DPW # _exptl.entry_id 6DPW _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 539.246 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 6DPW _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DPW _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 dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 ? _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 ? 5 O N N ? 5 R N N ? 5 U N N ? 5 V N N ? 5 W N N ? 5 X N 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 metalc ? metalc1 A OE2 GLU 71 A GLU 71 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc2 M O1G GTP . A GTP 501 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc3 M O1B GTP . A GTP 501 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc4 C OE2 GLU 71 C GLU 71 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc5 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc6 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc7 E OE2 GLU 71 E GLU 71 1_555 T MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc8 S O1G GTP . E GTP 501 1_555 T MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc9 S O1B GTP . E GTP 501 1_555 T MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc10 J OE2 GLU 71 J GLU 71 1_555 Z MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc11 Y O1G GTP . J GTP 501 1_555 Z MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc12 Y O1B GTP . J GTP 501 1_555 Z MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc13 K OE2 GLU 71 K GLU 71 1_555 BA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc14 AA O1G GTP . K GTP 501 1_555 BA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc15 AA O1B GTP . K GTP 501 1_555 BA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc16 L OE2 GLU 71 L GLU 71 1_555 DA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc17 CA O1G GTP . L GTP 501 1_555 DA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc18 CA O1B GTP . L GTP 501 1_555 DA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? # _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 129 n n PG S1G GSP doub 130 n n PG O2G GSP sing 131 n n PG O3G GSP sing 132 n n O3B PB GSP sing 133 n n O2G HOG2 GSP sing 134 n n O3G HOG3 GSP sing 135 n n PB O1B GSP doub 136 n n PB O2B GSP sing 137 n n PB O3A GSP sing 138 n n O2B HOB2 GSP sing 139 n n PA O1A GSP doub 140 n n PA O2A GSP sing 141 n n PA O3A GSP sing 142 n n PA O5' GSP sing 143 n n O2A HOA2 GSP sing 144 n n O5' C5' GSP sing 145 n n C5' C4' GSP sing 146 n n C5' "H5'1" GSP sing 147 n n C5' "H5'2" GSP sing 148 n n C4' O4' GSP sing 149 n n C4' C3' GSP sing 150 n n C4' H4' GSP sing 151 n n O4' C1' GSP sing 152 n n C3' O3' GSP sing 153 n n C3' C2' GSP sing 154 n n C3' H3' GSP sing 155 n n O3' HO3' GSP sing 156 n n C2' O2' GSP sing 157 n n C2' C1' GSP sing 158 n n C2' H2' GSP sing 159 n n O2' HO2' GSP sing 160 n n C1' N9 GSP sing 161 n n C1' H1' GSP sing 162 n n N9 C8 GSP sing 163 n y N9 C4 GSP sing 164 n y C8 N7 GSP doub 165 n y C8 H8 GSP sing 166 n n N7 C5 GSP sing 167 n y C5 C6 GSP sing 168 n n C5 C4 GSP doub 169 n y C6 O6 GSP doub 170 n n C6 N1 GSP sing 171 n n N1 C2 GSP sing 172 n n N1 HN1 GSP sing 173 n n C2 N2 GSP sing 174 n n C2 N3 GSP doub 175 n n N2 HN21 GSP sing 176 n n N2 HN22 GSP sing 177 n n N3 C4 GSP sing 178 n n # _atom_sites.entry_id 6DPW _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 M 3 GTP A 1 501 501 GTP GTP . N 4 MG A 1 502 502 MG MG . O 5 GSP B 1 501 501 GSP GSP . P 3 GTP C 1 501 501 GTP GTP . Q 4 MG C 1 502 502 MG MG . R 5 GSP D 1 501 501 GSP GSP . S 3 GTP E 1 501 501 GTP GTP . T 4 MG E 1 502 502 MG MG . U 5 GSP F 1 501 501 GSP GSP . V 5 GSP G 1 501 501 GSP GSP . W 5 GSP H 1 501 501 GSP GSP . X 5 GSP I 1 501 501 GSP GSP . Y 3 GTP J 1 501 501 GTP GTP . Z 4 MG J 1 502 502 MG MG . AA 3 GTP K 1 501 501 GTP GTP . BA 4 MG K 1 502 502 MG MG . CA 3 GTP L 1 501 501 GTP GTP . DA 4 MG L 1 502 502 MG MG . # 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 . . . W 5 338.419 460.649 308.701 1 34.37 ? PG GSP 501 H 1 HETATM 2 O O3B GSP . . . W 5 339.676 460.139 309.558 1 32.7 ? O3B GSP 501 H 1 HETATM 3 S S1G GSP . . . W 5 338.952 460.548 306.831 1 38.38 ? S1G GSP 501 H 1 HETATM 4 O O2G GSP . . . W 5 337.114 459.739 308.948 1 35.19 ? O2G GSP 501 H 1 HETATM 5 O O3G GSP . . . W 5 338.185 462.22 308.921 1 33.52 ? O3G GSP 501 H 1 HETATM 6 P PB GSP . . . W 5 339.49 459.956 311.135 1 30.7 ? PB GSP 501 H 1 HETATM 7 O O1B GSP . . . W 5 338.758 458.668 311.435 1 30.78 ? O1B GSP 501 H 1 HETATM 8 O O2B GSP . . . W 5 338.886 461.253 311.627 1 30.52 ? O2B GSP 501 H 1 HETATM 9 P PA GSP . . . W 5 341.934 458.666 311.348 1 27.87 ? PA GSP 501 H 1 HETATM 10 O O1A GSP . . . W 5 342.16 458.693 309.855 1 27.99 ? O1A GSP 501 H 1 HETATM 11 O O2A GSP . . . W 5 341.424 457.45 312.054 1 27.95 ? O2A GSP 501 H 1 HETATM 12 O O3A GSP . . . W 5 340.957 459.862 311.773 1 29.57 ? O3A GSP 501 H 1 HETATM 13 O O5' GSP . . . W 5 343.282 459.079 312.105 1 26.6 ? O5' GSP 501 H 1 HETATM 14 C C5' GSP . . . W 5 344.316 459.794 311.446 1 25.55 ? C5' GSP 501 H 1 HETATM 15 C C4' GSP . . . W 5 345.47 459.995 312.42 1 24.85 ? C4' GSP 501 H 1 HETATM 16 O O4' GSP . . . W 5 345.376 459.058 313.504 1 23.87 ? O4' GSP 501 H 1 HETATM 17 C C3' GSP . . . W 5 346.825 459.77 311.788 1 24.38 ? C3' GSP 501 H 1 HETATM 18 O O3' GSP . . . W 5 347.729 460.708 312.381 1 24.76 ? O3' GSP 501 H 1 HETATM 19 C C2' GSP . . . W 5 347.206 458.367 312.194 1 23.67 ? C2' GSP 501 H 1 HETATM 20 O O2' GSP . . . W 5 348.624 458.269 312.345 1 23.97 ? O2' GSP 501 H 1 HETATM 21 C C1' GSP . . . W 5 346.471 458.139 313.506 1 23.11 ? C1' GSP 501 H 1 HETATM 22 N N9 GSP . . . W 5 345.874 456.787 313.559 1 21.94 ? N9 GSP 501 H 1 HETATM 23 C C8 GSP . . . W 5 344.998 456.238 312.703 1 21.55 ? C8 GSP 501 H 1 HETATM 24 N N7 GSP . . . W 5 344.68 454.97 313.091 1 21.1 ? N7 GSP 501 H 1 HETATM 25 C C5 GSP . . . W 5 345.357 454.699 314.218 1 20.75 ? C5 GSP 501 H 1 HETATM 26 C C6 GSP . . . W 5 345.494 453.562 315.16 1 20.24 ? C6 GSP 501 H 1 HETATM 27 O O6 GSP . . . W 5 344.863 452.513 314.967 1 20.31 ? O6 GSP 501 H 1 HETATM 28 N N1 GSP . . . W 5 346.305 453.682 316.218 1 20.01 ? N1 GSP 501 H 1 HETATM 29 C C2 GSP . . . W 5 346.999 454.813 316.445 1 20.17 ? C2 GSP 501 H 1 HETATM 30 N N2 GSP . . . W 5 347.811 454.896 317.522 1 20.16 ? N2 GSP 501 H 1 HETATM 31 N N3 GSP . . . W 5 346.926 455.893 315.625 1 20.71 ? N3 GSP 501 H 1 HETATM 32 C C4 GSP . . . W 5 346.139 455.901 314.52 1 21.17 ? C4 GSP 501 H 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #