data_3JAK # _model_server_result.job_id 6Dg9qbCoBC1eKxIgyDTEeg _model_server_result.datetime_utc '2024-12-27 02:23:11' _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 3jak # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":501}' # _entry.id 3JAK # _exptl.entry_id 3JAK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 539.246 _entity.id 6 _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 3JAK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JAK _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 tetradecameric _pdbx_struct_assembly.oligomeric_count 14 _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,EA,FA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 Q N N ? 6 T N N ? 6 W N N ? 6 Z N N ? 6 CA N N ? 6 FA 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 E GLU 71 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc2 O O1B GTP . E GTP 501 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc3 O O1G GTP . E GTP 501 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc4 D OE2 GLU 71 J GLU 71 1_555 S MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc5 R O1G GTP . J GTP 501 1_555 S MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc6 R O1B GTP . J GTP 501 1_555 S MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc7 F OE2 GLU 71 C GLU 71 1_555 V MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc8 U O1B GTP . C GTP 501 1_555 V MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc9 U O1G GTP . C GTP 501 1_555 V MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc10 H OE2 GLU 71 L GLU 71 1_555 Y MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc11 X O1B GTP . L GTP 501 1_555 Y MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc12 X O1G GTP . L GTP 501 1_555 Y MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc13 J OE2 GLU 71 A GLU 71 1_555 BA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc14 AA O1B GTP . A GTP 501 1_555 BA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc15 AA O1G GTP . A GTP 501 1_555 BA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc16 M OE2 GLU 71 K GLU 71 1_555 EA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc17 DA O1B GTP . K GTP 501 1_555 EA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc18 DA O1G GTP . K GTP 501 1_555 EA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? # _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 3JAK _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 O 4 GTP E 1 501 501 GTP GTP . P 5 MG E 1 502 502 MG MG . Q 6 GSP F 1 501 501 GSP GSP . R 4 GTP J 1 501 501 GTP GTP . S 5 MG J 1 502 502 MG MG . T 6 GSP G 1 501 501 GSP GSP . U 4 GTP C 1 501 501 GTP GTP . V 5 MG C 1 502 502 MG MG . W 6 GSP D 1 501 501 GSP GSP . X 4 GTP L 1 501 501 GTP GTP . Y 5 MG L 1 502 502 MG MG . Z 6 GSP I 1 501 501 GSP GSP . AA 4 GTP A 1 501 501 GTP GTP . BA 5 MG A 1 502 502 MG MG . CA 6 GSP B 1 501 501 GSP GSP . DA 4 GTP K 1 501 501 GTP GTP . EA 5 MG K 1 502 502 MG MG . FA 6 GSP H 1 501 501 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 . . . Z 6 364.725 446.419 269.882 1 21.17 ? PG GSP 501 I 1 HETATM 2 O O3B GSP . . . Z 6 365.8 445.844 270.916 1 20.47 ? O3B GSP 501 I 1 HETATM 3 S S1G GSP . . . Z 6 365.265 445.684 268.148 1 22.03 ? S1G GSP 501 I 1 HETATM 4 O O2G GSP . . . Z 6 363.22 446.017 270.289 1 21.05 ? O2G GSP 501 I 1 HETATM 5 O O3G GSP . . . Z 6 364.94 448.012 269.753 1 20.95 ? O3G GSP 501 I 1 HETATM 6 P PB GSP . . . Z 6 365.595 446.054 272.485 1 19.8 ? PB GSP 501 I 1 HETATM 7 O O1B GSP . . . Z 6 365.293 447.507 272.758 1 19.97 ? O1B GSP 501 I 1 HETATM 8 O O2B GSP . . . Z 6 364.588 445.045 272.975 1 19.83 ? O2B GSP 501 I 1 HETATM 9 P PA GSP . . . Z 6 367.683 444.285 272.836 1 18.61 ? PA GSP 501 I 1 HETATM 10 O O1A GSP . . . Z 6 367.859 444.093 271.349 1 18.61 ? O1A GSP 501 I 1 HETATM 11 O O2A GSP . . . Z 6 366.936 443.284 273.675 1 18.64 ? O2A GSP 501 I 1 HETATM 12 O O3A GSP . . . Z 6 367.027 445.718 273.119 1 19.23 ? O3A GSP 501 I 1 HETATM 13 O O5' GSP . . . Z 6 369.121 444.473 273.521 1 18.11 ? O5' GSP 501 I 1 HETATM 14 C C5' GSP . . . Z 6 370.282 444.864 272.795 1 17.63 ? C5' GSP 501 I 1 HETATM 15 C C4' GSP . . . Z 6 371.495 444.704 273.708 1 17.31 ? C4' GSP 501 I 1 HETATM 16 O O4' GSP . . . Z 6 371.167 443.824 274.789 1 17.02 ? O4' GSP 501 I 1 HETATM 17 C C3' GSP . . . Z 6 372.7 444.095 273.022 1 17.14 ? C3' GSP 501 I 1 HETATM 18 O O3' GSP . . . Z 6 373.87 444.712 273.568 1 17.18 ? O3' GSP 501 I 1 HETATM 19 C C2' GSP . . . Z 6 372.652 442.631 273.411 1 16.97 ? C2' GSP 501 I 1 HETATM 20 O O2' GSP . . . Z 6 373.989 442.125 273.497 1 17.09 ? O2' GSP 501 I 1 HETATM 21 C C1' GSP . . . Z 6 371.936 442.616 274.757 1 16.8 ? C1' GSP 501 I 1 HETATM 22 N N9 GSP . . . Z 6 371.005 441.464 274.834 1 16.37 ? N9 GSP 501 I 1 HETATM 23 C C8 GSP . . . Z 6 369.997 441.176 273.996 1 16.23 ? C8 GSP 501 I 1 HETATM 24 N N7 GSP . . . Z 6 369.358 440.041 274.385 1 16.15 ? N7 GSP 501 I 1 HETATM 25 C C5 GSP . . . Z 6 369.953 439.587 275.5 1 16.08 ? C5 GSP 501 I 1 HETATM 26 C C6 GSP . . . Z 6 369.778 438.44 276.433 1 15.97 ? C6 GSP 501 I 1 HETATM 27 O O6 GSP . . . Z 6 368.881 437.594 276.256 1 15.87 ? O6 GSP 501 I 1 HETATM 28 N N1 GSP . . . Z 6 370.612 438.334 277.478 1 15.99 ? N1 GSP 501 I 1 HETATM 29 C C2 GSP . . . Z 6 371.596 439.237 277.704 1 16.12 ? C2 GSP 501 I 1 HETATM 30 N N2 GSP . . . Z 6 372.407 439.07 278.778 1 16.1 ? N2 GSP 501 I 1 HETATM 31 N N3 GSP . . . Z 6 371.815 440.31 276.887 1 16.15 ? N3 GSP 501 I 1 HETATM 32 C C4 GSP . . . Z 6 371.04 440.534 275.792 1 16.21 ? C4 GSP 501 I 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 66 _model_server_stats.query_time_ms 391 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #