data_4XSH # _model_server_result.job_id E_kpKZx85Cija26wRNgAxQ _model_server_result.datetime_utc '2024-11-24 15:58:43' _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 4xsh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 4XSH # _exptl.entry_id 4XSH _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 4XSH _cell.length_a 50.424 _cell.length_b 50.424 _cell.length_c 136.667 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XSH _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32' # _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,G,H,I,J _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 metalc ? metalc1 A OG1 THR 19 A THR 19 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc2 A O THR 37 A THR 37 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc3 C O2G GSP . A GSP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc4 C O1B GSP . A GSP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc5 D MG MG . A MG 202 1_555 I O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? metalc ? metalc6 D MG MG . A MG 202 1_555 I O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? # _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 138 n n PG S1G GSP doub 139 n n PG O2G GSP sing 140 n n PG O3G GSP sing 141 n n O3B PB GSP sing 142 n n O2G HOG2 GSP sing 143 n n O3G HOG3 GSP sing 144 n n PB O1B GSP doub 145 n n PB O2B GSP sing 146 n n PB O3A GSP sing 147 n n O2B HOB2 GSP sing 148 n n PA O1A GSP doub 149 n n PA O2A GSP sing 150 n n PA O3A GSP sing 151 n n PA O5' GSP sing 152 n n O2A HOA2 GSP sing 153 n n O5' C5' GSP sing 154 n n C5' C4' GSP sing 155 n n C5' "H5'1" GSP sing 156 n n C5' "H5'2" GSP sing 157 n n C4' O4' GSP sing 158 n n C4' C3' GSP sing 159 n n C4' H4' GSP sing 160 n n O4' C1' GSP sing 161 n n C3' O3' GSP sing 162 n n C3' C2' GSP sing 163 n n C3' H3' GSP sing 164 n n O3' HO3' GSP sing 165 n n C2' O2' GSP sing 166 n n C2' C1' GSP sing 167 n n C2' H2' GSP sing 168 n n O2' HO2' GSP sing 169 n n C1' N9 GSP sing 170 n n C1' H1' GSP sing 171 n n N9 C8 GSP sing 172 n y N9 C4 GSP sing 173 n y C8 N7 GSP doub 174 n y C8 H8 GSP sing 175 n n N7 C5 GSP sing 176 n y C5 C6 GSP sing 177 n n C5 C4 GSP doub 178 n y C6 O6 GSP doub 179 n n C6 N1 GSP sing 180 n n N1 C2 GSP sing 181 n n N1 HN1 GSP sing 182 n n C2 N2 GSP sing 183 n n C2 N3 GSP doub 184 n n N2 HN21 GSP sing 185 n n N2 HN22 GSP sing 186 n n N3 C4 GSP sing 187 n n # _atom_sites.entry_id 4XSH _atom_sites.fract_transf_matrix[1][1] 0.019832 _atom_sites.fract_transf_matrix[1][2] 0.01145 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0229 _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] 0.007317 _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 1 201 538 GSP GSP . D 4 MG A 1 202 1 MG MG . E 5 NAI B 1 301 1 NAI NAI . F 6 EDO B 1 302 1 EDO EDO . G 6 EDO B 1 303 3 EDO EDO . H 6 EDO B 1 304 4 EDO EDO . I 7 HOH A 1 301 443 HOH HOH . I 7 HOH A 2 302 158 HOH HOH . I 7 HOH A 3 303 428 HOH HOH . I 7 HOH A 4 304 271 HOH HOH . I 7 HOH A 5 305 402 HOH HOH . I 7 HOH A 6 306 509 HOH HOH . I 7 HOH A 7 307 343 HOH HOH . I 7 HOH A 8 308 239 HOH HOH . I 7 HOH A 9 309 382 HOH HOH . I 7 HOH A 10 310 406 HOH HOH . I 7 HOH A 11 311 358 HOH HOH . I 7 HOH A 12 312 383 HOH HOH . I 7 HOH A 13 313 512 HOH HOH . I 7 HOH A 14 314 344 HOH HOH . I 7 HOH A 15 315 511 HOH HOH . I 7 HOH A 16 316 384 HOH HOH . I 7 HOH A 17 317 345 HOH HOH . I 7 HOH A 18 318 348 HOH HOH . I 7 HOH A 19 319 362 HOH HOH . I 7 HOH A 20 320 424 HOH HOH . I 7 HOH A 21 321 347 HOH HOH . I 7 HOH A 22 322 223 HOH HOH . I 7 HOH A 23 323 507 HOH HOH . I 7 HOH A 24 324 131 HOH HOH . I 7 HOH A 25 325 134 HOH HOH . I 7 HOH A 26 326 510 HOH HOH . I 7 HOH A 27 327 371 HOH HOH . I 7 HOH A 28 328 373 HOH HOH . I 7 HOH A 29 329 421 HOH HOH . I 7 HOH A 30 330 354 HOH HOH . J 7 HOH B 1 401 489 HOH HOH . J 7 HOH B 2 402 506 HOH HOH . J 7 HOH B 3 403 473 HOH HOH . J 7 HOH B 4 404 518 HOH HOH . J 7 HOH B 5 405 516 HOH HOH . J 7 HOH B 6 406 393 HOH HOH . J 7 HOH B 7 407 514 HOH HOH . J 7 HOH B 8 408 515 HOH HOH . J 7 HOH B 9 409 504 HOH HOH . J 7 HOH B 10 410 503 HOH HOH . J 7 HOH B 11 411 419 HOH HOH . J 7 HOH B 12 412 319 HOH HOH . J 7 HOH B 13 413 100 HOH HOH . J 7 HOH B 14 414 357 HOH HOH . J 7 HOH B 15 415 427 HOH HOH . J 7 HOH B 16 416 492 HOH HOH . J 7 HOH B 17 417 189 HOH HOH . J 7 HOH B 18 418 487 HOH HOH . J 7 HOH B 19 419 162 HOH HOH . J 7 HOH B 20 420 372 HOH HOH . J 7 HOH B 21 421 505 HOH HOH . J 7 HOH B 22 422 185 HOH HOH . J 7 HOH B 23 423 513 HOH HOH . J 7 HOH B 24 424 456 HOH HOH . J 7 HOH B 25 425 508 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 -0.235 20.056 21.371 1 65.75 ? PG GSP 201 A 1 HETATM 2 O O3B GSP . . . C 3 0.084 19.007 22.576 1 58.59 ? O3B GSP 201 A 1 HETATM 3 S S1G GSP . . . C 3 1.151 19.696 20.03 1 71.8 ? S1G GSP 201 A 1 HETATM 4 O O2G GSP . . . C 3 -1.695 19.889 20.82 1 58.46 ? O2G GSP 201 A 1 HETATM 5 O O3G GSP . . . C 3 -0.201 21.568 21.883 1 60.37 ? O3G GSP 201 A 1 HETATM 6 P PB GSP . . . C 3 -0.867 18.633 23.777 1 52.96 ? PB GSP 201 A 1 HETATM 7 O O1B GSP . . . C 3 -2.277 18.425 23.34 1 56.78 ? O1B GSP 201 A 1 HETATM 8 O O2B GSP . . . C 3 -0.685 19.644 24.834 1 45.55 ? O2B GSP 201 A 1 HETATM 9 P PA GSP . . . C 3 -1.057 15.842 24.164 1 50.08 ? PA GSP 201 A 1 HETATM 10 O O1A GSP . . . C 3 -1.393 15.58 22.736 1 46.11 ? O1A GSP 201 A 1 HETATM 11 O O2A GSP . . . C 3 -2.243 15.875 25.057 1 51.91 ? O2A GSP 201 A 1 HETATM 12 O O3A GSP . . . C 3 -0.29 17.237 24.34 1 51.64 ? O3A GSP 201 A 1 HETATM 13 O O5' GSP . . . C 3 0.017 14.819 24.8 1 50.67 ? O5' GSP 201 A 1 HETATM 14 C C5' GSP . . . C 3 1.321 14.755 24.255 1 53.21 ? C5' GSP 201 A 1 HETATM 15 C C4' GSP . . . C 3 1.904 13.367 24.456 1 56.02 ? C4' GSP 201 A 1 HETATM 16 O O4' GSP . . . C 3 2.076 13.124 25.855 1 52.96 ? O4' GSP 201 A 1 HETATM 17 C C3' GSP . . . C 3 1.02 12.26 23.894 1 55.5 ? C3' GSP 201 A 1 HETATM 18 O O3' GSP . . . C 3 1.841 11.244 23.339 1 65.97 ? O3' GSP 201 A 1 HETATM 19 C C2' GSP . . . C 3 0.336 11.685 25.112 1 55.52 ? C2' GSP 201 A 1 HETATM 20 O O2' GSP . . . C 3 0.12 10.305 24.98 1 51.47 ? O2' GSP 201 A 1 HETATM 21 C C1' GSP . . . C 3 1.345 11.967 26.228 1 53.43 ? C1' GSP 201 A 1 HETATM 22 N N9 GSP . . . C 3 0.628 12.204 27.49 1 52.5 ? N9 GSP 201 A 1 HETATM 23 C C8 GSP . . . C 3 -0.472 13.006 27.658 1 52.8 ? C8 GSP 201 A 1 HETATM 24 N N7 GSP . . . C 3 -0.857 12.951 28.951 1 50.62 ? N7 GSP 201 A 1 HETATM 25 C C5 GSP . . . C 3 -0.009 12.116 29.604 1 52.08 ? C5 GSP 201 A 1 HETATM 26 C C6 GSP . . . C 3 0.071 11.714 30.936 1 52.41 ? C6 GSP 201 A 1 HETATM 27 O O6 GSP . . . C 3 -0.74 12.179 31.736 1 47.29 ? O6 GSP 201 A 1 HETATM 28 N N1 GSP . . . C 3 1.064 10.85 31.339 1 54.87 ? N1 GSP 201 A 1 HETATM 29 C C2 GSP . . . C 3 1.999 10.387 30.429 1 52.66 ? C2 GSP 201 A 1 HETATM 30 N N2 GSP . . . C 3 2.978 9.545 30.806 1 47.99 ? N2 GSP 201 A 1 HETATM 31 N N3 GSP . . . C 3 1.901 10.784 29.102 1 52.28 ? N3 GSP 201 A 1 HETATM 32 C C4 GSP . . . C 3 0.941 11.651 28.706 1 50.24 ? C4 GSP 201 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #