data_1CJK # _model_server_result.job_id zDH2crnPF1NOAcuzaMWZvA _model_server_result.datetime_utc '2024-10-26 18:20:04' _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 1cjk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":405}' # _entry.id 1CJK # _exptl.entry_id 1CJK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 10 _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 90 _cell.entry_id 1CJK _cell.length_a 118.9 _cell.length_b 134.9 _cell.length_c 72.2 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CJK _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,G,H,I,J,K,L,M,N _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 10 _struct_asym.id K _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 metalc ? metalc1 L O HOH . A HOH 53 1_555 D MG MG . A MG 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc2 A OD1 ASP 33 A ASP 396 1_555 D MG MG . A MG 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc3 A OD2 ASP 33 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc4 A O ILE 34 A ILE 397 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc5 A OD1 ASP 77 A ASP 440 1_555 D MG MG . A MG 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc6 A OD2 ASP 77 A ASP 440 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc7 D MG MG . A MG 581 1_555 G O5' TAT . A TAT 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc8 E MN MN . A MN 582 1_555 G O2B TAT . A TAT 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc9 E MN MN . A MN 582 1_555 G O1A TAT . A TAT 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc10 C OG SER 54 C SER 54 1_555 I MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc11 C OG1 THR 204 C THR 204 1_555 I MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc12 I MG MG . C MG 403 1_555 K O2G GSP . C GSP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.722 ? metalc ? metalc13 I MG MG . C MG 403 1_555 K O2B GSP . C GSP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc14 I MG MG . C MG 403 1_555 N O HOH . C HOH 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc15 I MG MG . C MG 403 1_555 N O HOH . C HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _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 194 n n PG S1G GSP doub 195 n n PG O2G GSP sing 196 n n PG O3G GSP sing 197 n n O3B PB GSP sing 198 n n O2G HOG2 GSP sing 199 n n O3G HOG3 GSP sing 200 n n PB O1B GSP doub 201 n n PB O2B GSP sing 202 n n PB O3A GSP sing 203 n n O2B HOB2 GSP sing 204 n n PA O1A GSP doub 205 n n PA O2A GSP sing 206 n n PA O3A GSP sing 207 n n PA O5' GSP sing 208 n n O2A HOA2 GSP sing 209 n n O5' C5' GSP sing 210 n n C5' C4' GSP sing 211 n n C5' "H5'1" GSP sing 212 n n C5' "H5'2" GSP sing 213 n n C4' O4' GSP sing 214 n n C4' C3' GSP sing 215 n n C4' H4' GSP sing 216 n n O4' C1' GSP sing 217 n n C3' O3' GSP sing 218 n n C3' C2' GSP sing 219 n n C3' H3' GSP sing 220 n n O3' HO3' GSP sing 221 n n C2' O2' GSP sing 222 n n C2' C1' GSP sing 223 n n C2' H2' GSP sing 224 n n O2' HO2' GSP sing 225 n n C1' N9 GSP sing 226 n n C1' H1' GSP sing 227 n n N9 C8 GSP sing 228 n y N9 C4 GSP sing 229 n y C8 N7 GSP doub 230 n y C8 H8 GSP sing 231 n n N7 C5 GSP sing 232 n y C5 C6 GSP sing 233 n n C5 C4 GSP doub 234 n y C6 O6 GSP doub 235 n n C6 N1 GSP sing 236 n n N1 C2 GSP sing 237 n n N1 HN1 GSP sing 238 n n C2 N2 GSP sing 239 n n C2 N3 GSP doub 240 n n N2 HN21 GSP sing 241 n n N2 HN22 GSP sing 242 n n N3 C4 GSP sing 243 n n # _atom_sites.entry_id 1CJK _atom_sites.fract_transf_matrix[1][1] 0.00841 _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] 0.007413 _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] 0.01385 _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 D 4 MG A 1 581 502 MG MG . E 5 MN A 1 582 503 MN MN . F 6 FOK A 1 701 701 FOK FOK . G 7 TAT A 1 801 801 TAT AGS . H 8 MES A 1 901 901 MES MES . I 4 MG C 1 403 396 MG MG . J 9 CL C 1 404 397 CL CL . K 10 GSP C 1 405 395 GSP GSP . L 11 HOH A 1 11 11 HOH HOH . L 11 HOH A 2 24 24 HOH HOH . L 11 HOH A 3 25 25 HOH HOH . L 11 HOH A 4 27 27 HOH HOH . L 11 HOH A 5 30 30 HOH HOH . L 11 HOH A 6 31 31 HOH HOH . L 11 HOH A 7 33 33 HOH HOH . L 11 HOH A 8 53 53 HOH HOH . M 11 HOH B 1 8 8 HOH HOH . M 11 HOH B 2 9 9 HOH HOH . M 11 HOH B 3 13 13 HOH HOH . M 11 HOH B 4 14 14 HOH HOH . M 11 HOH B 5 15 15 HOH HOH . M 11 HOH B 6 16 16 HOH HOH . M 11 HOH B 7 17 17 HOH HOH . M 11 HOH B 8 18 18 HOH HOH . M 11 HOH B 9 19 19 HOH HOH . M 11 HOH B 10 22 22 HOH HOH . M 11 HOH B 11 26 26 HOH HOH . M 11 HOH B 12 36 36 HOH HOH . N 11 HOH C 1 406 2 HOH HOH . N 11 HOH C 2 407 3 HOH HOH . N 11 HOH C 3 408 7 HOH HOH . N 11 HOH C 4 409 10 HOH HOH . N 11 HOH C 5 410 34 HOH HOH . N 11 HOH C 6 411 39 HOH HOH . N 11 HOH C 7 412 40 HOH HOH . N 11 HOH C 8 413 41 HOH HOH . N 11 HOH C 9 414 43 HOH HOH . N 11 HOH C 10 415 44 HOH HOH . N 11 HOH C 11 416 45 HOH HOH . N 11 HOH C 12 417 49 HOH HOH . N 11 HOH C 13 418 51 HOH HOH . N 11 HOH C 14 419 52 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 . . . K 10 23.685 3.102 29.357 1 36.88 ? PG GSP 405 C 1 HETATM 2 O O3B GSP . . . K 10 22.558 3.376 28.374 1 31.19 ? O3B GSP 405 C 1 HETATM 3 S S1G GSP . . . K 10 25.111 4.332 29.211 1 37.48 ? S1G GSP 405 C 1 HETATM 4 O O2G GSP . . . K 10 23.195 3.386 30.737 1 34.77 ? O2G GSP 405 C 1 HETATM 5 O O3G GSP . . . K 10 24.243 1.759 29.049 1 36.98 ? O3G GSP 405 C 1 HETATM 6 P PB GSP . . . K 10 21.269 2.661 28.059 1 26.62 ? PB GSP 405 C 1 HETATM 7 O O1B GSP . . . K 10 21.554 1.545 27.126 1 20.26 ? O1B GSP 405 C 1 HETATM 8 O O2B GSP . . . K 10 20.574 2.386 29.328 1 25.42 ? O2B GSP 405 C 1 HETATM 9 P PA GSP . . . K 10 19.277 4.46 27.742 1 26.67 ? PA GSP 405 C 1 HETATM 10 O O1A GSP . . . K 10 18.285 3.457 28.203 1 24.07 ? O1A GSP 405 C 1 HETATM 11 O O2A GSP . . . K 10 19.682 5.578 28.633 1 22.85 ? O2A GSP 405 C 1 HETATM 12 O O3A GSP . . . K 10 20.51 3.725 27.325 1 26.61 ? O3A GSP 405 C 1 HETATM 13 O O5' GSP . . . K 10 18.725 5.106 26.392 1 26.66 ? O5' GSP 405 C 1 HETATM 14 C C5' GSP . . . K 10 19.437 6.177 25.747 1 27.3 ? C5' GSP 405 C 1 HETATM 15 C C4' GSP . . . K 10 18.482 7.165 25.114 1 23.71 ? C4' GSP 405 C 1 HETATM 16 O O4' GSP . . . K 10 17.839 6.607 23.944 1 23.64 ? O4' GSP 405 C 1 HETATM 17 C C3' GSP . . . K 10 17.351 7.633 26.019 1 24.47 ? C3' GSP 405 C 1 HETATM 18 O O3' GSP . . . K 10 17.141 9.033 25.813 1 25.39 ? O3' GSP 405 C 1 HETATM 19 C C2' GSP . . . K 10 16.168 6.831 25.512 1 22.93 ? C2' GSP 405 C 1 HETATM 20 O O2' GSP . . . K 10 14.933 7.454 25.73 1 28.07 ? O2' GSP 405 C 1 HETATM 21 C C1' GSP . . . K 10 16.439 6.763 24.04 1 21.21 ? C1' GSP 405 C 1 HETATM 22 N N9 GSP . . . K 10 15.805 5.631 23.371 1 21.89 ? N9 GSP 405 C 1 HETATM 23 C C8 GSP . . . K 10 15.869 4.315 23.741 1 23.55 ? C8 GSP 405 C 1 HETATM 24 N N7 GSP . . . K 10 15.18 3.532 22.954 1 24.83 ? N7 GSP 405 C 1 HETATM 25 C C5 GSP . . . K 10 14.629 4.384 22.008 1 21.15 ? C5 GSP 405 C 1 HETATM 26 C C6 GSP . . . K 10 13.783 4.109 20.913 1 19.67 ? C6 GSP 405 C 1 HETATM 27 O O6 GSP . . . K 10 13.339 3.03 20.548 1 22.19 ? O6 GSP 405 C 1 HETATM 28 N N1 GSP . . . K 10 13.456 5.252 20.214 1 18.96 ? N1 GSP 405 C 1 HETATM 29 C C2 GSP . . . K 10 13.889 6.506 20.52 1 22.02 ? C2 GSP 405 C 1 HETATM 30 N N2 GSP . . . K 10 13.465 7.513 19.708 1 17.34 ? N2 GSP 405 C 1 HETATM 31 N N3 GSP . . . K 10 14.686 6.775 21.549 1 23.9 ? N3 GSP 405 C 1 HETATM 32 C C4 GSP . . . K 10 15.01 5.676 22.243 1 21.15 ? C4 GSP 405 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 32 #