data_1U0H # _model_server_result.job_id t-0JSBVWl8ZLRgJgPmMYRg _model_server_result.datetime_utc '2024-11-23 10:26:56' _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 1u0h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":395}' # _entry.id 1U0H # _exptl.entry_id 1U0H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 8 _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 1U0H _cell.length_a 118.4 _cell.length_b 133 _cell.length_c 70.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1U0H _symmetry.cell_setting ? _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 _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 8 _struct_asym.id J _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 G O2A ONM . A ONM 100 1_555 D MG MG . A MG 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.072 ? metalc ? metalc2 G O3B ONM . A ONM 100 1_555 D MG MG . A MG 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc3 G O1B ONM . A ONM 100 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc4 G O1G ONM . A ONM 100 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc5 A OD1 ASP 41 A ASP 396 1_555 D MG MG . A MG 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.106 ? metalc ? metalc6 A OD2 ASP 41 A ASP 396 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc7 A O ILE 42 A ILE 397 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc8 A N GLU 43 A GLU 398 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.092 ? metalc ? metalc9 A OD1 ASP 85 A ASP 440 1_555 D MG MG . A MG 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc10 A OD2 ASP 85 A ASP 440 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc11 C OG SER 54 C SER 54 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc12 C OG1 THR 204 C THR 204 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc13 J O2G GSP . C GSP 395 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc14 J O3G GSP . C GSP 395 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc15 J O2B GSP . C GSP 395 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? # _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 1U0H _atom_sites.fract_transf_matrix[1][1] 0.008446 _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] 0.007519 _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] 0.014205 _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 4 MG A 1 582 503 MG MG . F 5 FOK A 1 101 101 FOK FOK . G 6 ONM A 1 100 100 ONM ONM . H 4 MG C 1 396 396 MG MG . I 7 CL C 1 397 397 CL CL . J 8 GSP C 1 395 395 GSP GSP . K 9 HOH A 1 17 17 HOH HOH . K 9 HOH A 2 19 19 HOH HOH . K 9 HOH A 3 37 37 HOH HOH . K 9 HOH A 4 38 38 HOH HOH . L 9 HOH B 1 8 8 HOH HOH . L 9 HOH B 2 15 15 HOH HOH . L 9 HOH B 3 18 18 HOH HOH . L 9 HOH B 4 22 22 HOH HOH . L 9 HOH B 5 26 26 HOH HOH . L 9 HOH B 6 32 32 HOH HOH . L 9 HOH B 7 58 58 HOH HOH . M 9 HOH C 1 398 1 HOH HOH . M 9 HOH C 2 399 2 HOH HOH . M 9 HOH C 3 400 3 HOH HOH . M 9 HOH C 4 401 7 HOH HOH . M 9 HOH C 5 402 39 HOH HOH . M 9 HOH C 6 403 51 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 . . . J 8 23.266 3.314 29.103 1 66.87 ? PG GSP 395 C 1 HETATM 2 O O3B GSP . . . J 8 22.489 3.319 27.649 1 57.02 ? O3B GSP 395 C 1 HETATM 3 S S1G GSP . . . J 8 24.894 4.156 28.699 1 65.71 ? S1G GSP 395 C 1 HETATM 4 O O2G GSP . . . J 8 22.218 3.984 29.919 1 66.25 ? O2G GSP 395 C 1 HETATM 5 O O3G GSP . . . J 8 23.77 1.941 29.463 1 67.57 ? O3G GSP 395 C 1 HETATM 6 P PB GSP . . . J 8 20.957 2.67 27.455 1 45.33 ? PB GSP 395 C 1 HETATM 7 O O1B GSP . . . J 8 21.284 1.456 26.725 1 43.08 ? O1B GSP 395 C 1 HETATM 8 O O2B GSP . . . J 8 20.124 2.417 28.662 1 44.51 ? O2B GSP 395 C 1 HETATM 9 P PA GSP . . . J 8 18.798 4.483 27.097 1 44.11 ? PA GSP 395 C 1 HETATM 10 O O1A GSP . . . J 8 17.721 3.499 27.391 1 44.03 ? O1A GSP 395 C 1 HETATM 11 O O2A GSP . . . J 8 19.278 5.483 28.107 1 42.71 ? O2A GSP 395 C 1 HETATM 12 O O3A GSP . . . J 8 20.073 3.715 26.568 1 45.36 ? O3A GSP 395 C 1 HETATM 13 O O5' GSP . . . J 8 18.296 5.351 25.801 1 38.7 ? O5' GSP 395 C 1 HETATM 14 C C5' GSP . . . J 8 19.07 6.439 25.198 1 38.74 ? C5' GSP 395 C 1 HETATM 15 C C4' GSP . . . J 8 18.069 7.386 24.563 1 37.06 ? C4' GSP 395 C 1 HETATM 16 O O4' GSP . . . J 8 17.349 6.718 23.457 1 37.11 ? O4' GSP 395 C 1 HETATM 17 C C3' GSP . . . J 8 16.931 7.826 25.55 1 38.81 ? C3' GSP 395 C 1 HETATM 18 O O3' GSP . . . J 8 16.864 9.278 25.495 1 43.92 ? O3' GSP 395 C 1 HETATM 19 C C2' GSP . . . J 8 15.609 7.171 24.961 1 36.35 ? C2' GSP 395 C 1 HETATM 20 O O2' GSP . . . J 8 14.462 8.008 25.14 1 43.33 ? O2' GSP 395 C 1 HETATM 21 C C1' GSP . . . J 8 15.927 6.991 23.456 1 33.8 ? C1' GSP 395 C 1 HETATM 22 N N9 GSP . . . J 8 15.317 5.787 22.819 1 29.05 ? N9 GSP 395 C 1 HETATM 23 C C8 GSP . . . J 8 15.34 4.444 23.118 1 26.35 ? C8 GSP 395 C 1 HETATM 24 N N7 GSP . . . J 8 14.685 3.665 22.315 1 23.16 ? N7 GSP 395 C 1 HETATM 25 C C5 GSP . . . J 8 14.173 4.565 21.388 1 24.03 ? C5 GSP 395 C 1 HETATM 26 C C6 GSP . . . J 8 13.35 4.281 20.231 1 25.03 ? C6 GSP 395 C 1 HETATM 27 O O6 GSP . . . J 8 13 3.139 19.927 1 24.49 ? O6 GSP 395 C 1 HETATM 28 N N1 GSP . . . J 8 13.043 5.474 19.562 1 24.78 ? N1 GSP 395 C 1 HETATM 29 C C2 GSP . . . J 8 13.453 6.768 19.924 1 29.66 ? C2 GSP 395 C 1 HETATM 30 N N2 GSP . . . J 8 13.091 7.804 19.202 1 33.75 ? N2 GSP 395 C 1 HETATM 31 N N3 GSP . . . J 8 14.233 7.014 21.013 1 30.02 ? N3 GSP 395 C 1 HETATM 32 C C4 GSP . . . J 8 14.553 5.864 21.695 1 26.42 ? C4 GSP 395 C 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #