data_8E0D # _model_server_result.job_id ZGPK3_Va0BG_M5HrDz-R0A _model_server_result.datetime_utc '2024-11-29 10:38:38' _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 8e0d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8E0D # _exptl.entry_id 8E0D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 603.16 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5',3'-TETRAPHOSPHATE" _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 101.63 _cell.angle_gamma 90 _cell.entry_id 8E0D _cell.length_a 90.828 _cell.length_b 38.42 _cell.length_c 55.607 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E0D _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H17 N5 O17 P4' _chem_comp.formula_weight 603.16 _chem_comp.id G4P _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5',3'-TETRAPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms 'guanosine tetraphosphate;ppGpp' # 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 PB O1B G4P doub 83 n n PB O2B G4P sing 84 n n PB O3B G4P sing 85 n n PB O3A G4P sing 86 n n O2B HOB2 G4P sing 87 n n O3B HOB3 G4P sing 88 n n O3A PA G4P sing 89 n n PA O1A G4P doub 90 n n PA O2A G4P sing 91 n n PA O5' G4P sing 92 n n O2A HOA2 G4P sing 93 n n O5' C5' G4P sing 94 n n C5' C4' G4P sing 95 n n C5' H5' G4P sing 96 n n C5' "H5''" G4P sing 97 n n C4' O4' G4P sing 98 n n C4' C3' G4P sing 99 n n C4' H4' G4P sing 100 n n O4' C1' G4P sing 101 n n C3' O3' G4P sing 102 n n C3' C2' G4P sing 103 n n C3' H3' G4P sing 104 n n O3' PC G4P sing 105 n n C2' O2' G4P sing 106 n n C2' C1' G4P sing 107 n n C2' H2' G4P sing 108 n n O2' HO2' G4P sing 109 n n C1' N9 G4P sing 110 n n C1' H1' G4P sing 111 n n N9 C8 G4P sing 112 n y N9 C4 G4P sing 113 n y C8 N7 G4P doub 114 n y C8 H8 G4P sing 115 n n N7 C5 G4P sing 116 n y C5 C6 G4P sing 117 n n C5 C4 G4P doub 118 n y C6 O6 G4P doub 119 n n C6 N1 G4P sing 120 n n N1 C2 G4P sing 121 n n N1 HN1 G4P sing 122 n n C2 N2 G4P sing 123 n n C2 N3 G4P doub 124 n n N2 HN21 G4P sing 125 n n N2 HN22 G4P sing 126 n n N3 C4 G4P sing 127 n n PC O1C G4P doub 128 n n PC O2C G4P sing 129 n n PC O3C G4P sing 130 n n O2C H2C G4P sing 131 n n O3C PD G4P sing 132 n n PD O1D G4P doub 133 n n PD O2D G4P sing 134 n n PD O3D G4P sing 135 n n O2D H2D G4P sing 136 n n O3D H3D G4P sing 137 n n # _atom_sites.entry_id 8E0D _atom_sites.fract_transf_matrix[1][1] 0.01101 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002266 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026028 _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] 0.01836 _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 B 2 G4P A 1 201 1 G4P G4P . C 3 HOH A 1 301 14 HOH HOH . C 3 HOH A 2 302 5 HOH HOH . C 3 HOH A 3 303 72 HOH HOH . C 3 HOH A 4 304 36 HOH HOH . C 3 HOH A 5 305 27 HOH HOH . C 3 HOH A 6 306 83 HOH HOH . C 3 HOH A 7 307 19 HOH HOH . C 3 HOH A 8 308 71 HOH HOH . C 3 HOH A 9 309 63 HOH HOH . C 3 HOH A 10 310 25 HOH HOH . C 3 HOH A 11 311 48 HOH HOH . C 3 HOH A 12 312 10 HOH HOH . C 3 HOH A 13 313 11 HOH HOH . C 3 HOH A 14 314 7 HOH HOH . C 3 HOH A 15 315 88 HOH HOH . C 3 HOH A 16 316 26 HOH HOH . C 3 HOH A 17 317 1 HOH HOH . C 3 HOH A 18 318 44 HOH HOH . C 3 HOH A 19 319 34 HOH HOH . C 3 HOH A 20 320 45 HOH HOH . C 3 HOH A 21 321 20 HOH HOH . C 3 HOH A 22 322 9 HOH HOH . C 3 HOH A 23 323 16 HOH HOH . C 3 HOH A 24 324 106 HOH HOH . C 3 HOH A 25 325 95 HOH HOH . C 3 HOH A 26 326 37 HOH HOH . C 3 HOH A 27 327 2 HOH HOH . C 3 HOH A 28 328 60 HOH HOH . C 3 HOH A 29 329 35 HOH HOH . C 3 HOH A 30 330 103 HOH HOH . C 3 HOH A 31 331 70 HOH HOH . C 3 HOH A 32 332 31 HOH HOH . C 3 HOH A 33 333 4 HOH HOH . C 3 HOH A 34 334 18 HOH HOH . C 3 HOH A 35 335 61 HOH HOH . C 3 HOH A 36 336 57 HOH HOH . C 3 HOH A 37 337 32 HOH HOH . C 3 HOH A 38 338 33 HOH HOH . C 3 HOH A 39 339 74 HOH HOH . C 3 HOH A 40 340 55 HOH HOH . C 3 HOH A 41 341 87 HOH HOH . C 3 HOH A 42 342 13 HOH HOH . C 3 HOH A 43 343 68 HOH HOH . C 3 HOH A 44 344 22 HOH HOH . C 3 HOH A 45 345 40 HOH HOH . C 3 HOH A 46 346 43 HOH HOH . C 3 HOH A 47 347 46 HOH HOH . C 3 HOH A 48 348 42 HOH HOH . C 3 HOH A 49 349 29 HOH HOH . C 3 HOH A 50 350 28 HOH HOH . C 3 HOH A 51 351 39 HOH HOH . C 3 HOH A 52 352 82 HOH HOH . C 3 HOH A 53 353 47 HOH HOH . C 3 HOH A 54 354 69 HOH HOH . C 3 HOH A 55 355 12 HOH HOH . C 3 HOH A 56 356 6 HOH HOH . C 3 HOH A 57 357 38 HOH HOH . C 3 HOH A 58 358 66 HOH HOH . C 3 HOH A 59 359 23 HOH HOH . C 3 HOH A 60 360 94 HOH HOH . C 3 HOH A 61 361 51 HOH HOH . C 3 HOH A 62 362 102 HOH HOH . C 3 HOH A 63 363 52 HOH HOH . C 3 HOH A 64 364 30 HOH HOH . C 3 HOH A 65 365 24 HOH HOH . C 3 HOH A 66 366 56 HOH HOH . C 3 HOH A 67 367 17 HOH HOH . C 3 HOH A 68 368 41 HOH HOH . C 3 HOH A 69 369 78 HOH HOH . C 3 HOH A 70 370 3 HOH HOH . C 3 HOH A 71 371 86 HOH HOH . C 3 HOH A 72 372 59 HOH HOH . C 3 HOH A 73 373 8 HOH HOH . C 3 HOH A 74 374 115 HOH HOH . C 3 HOH A 75 375 80 HOH HOH . C 3 HOH A 76 376 91 HOH HOH . C 3 HOH A 77 377 89 HOH HOH . C 3 HOH A 78 378 64 HOH HOH . C 3 HOH A 79 379 77 HOH HOH . C 3 HOH A 80 380 49 HOH HOH . C 3 HOH A 81 381 21 HOH HOH . C 3 HOH A 82 382 114 HOH HOH . C 3 HOH A 83 383 75 HOH HOH . C 3 HOH A 84 384 73 HOH HOH . C 3 HOH A 85 385 53 HOH HOH . C 3 HOH A 86 386 104 HOH HOH . C 3 HOH A 87 387 96 HOH HOH . C 3 HOH A 88 388 85 HOH HOH . C 3 HOH A 89 389 76 HOH HOH . C 3 HOH A 90 390 107 HOH HOH . C 3 HOH A 91 391 113 HOH HOH . C 3 HOH A 92 392 110 HOH HOH . C 3 HOH A 93 393 62 HOH HOH . C 3 HOH A 94 394 67 HOH HOH . C 3 HOH A 95 395 100 HOH HOH . C 3 HOH A 96 396 112 HOH HOH . C 3 HOH A 97 397 108 HOH HOH . C 3 HOH A 98 398 81 HOH HOH . C 3 HOH A 99 399 111 HOH HOH . C 3 HOH A 100 400 105 HOH HOH . C 3 HOH A 101 401 99 HOH HOH . C 3 HOH A 102 402 50 HOH HOH . C 3 HOH A 103 403 116 HOH HOH . C 3 HOH A 104 404 93 HOH HOH . C 3 HOH A 105 405 101 HOH HOH . C 3 HOH A 106 406 98 HOH HOH . C 3 HOH A 107 407 90 HOH HOH . C 3 HOH A 108 408 65 HOH HOH . C 3 HOH A 109 409 109 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 PB G4P . . . B 2 27.421 12.707 346.309 1 15.66 ? PB G4P 201 A 1 HETATM 2 O O1B G4P . . . B 2 27.786 11.931 345.057 1 15.33 ? O1B G4P 201 A 1 HETATM 3 O O2B G4P . . . B 2 28.623 13.448 346.836 1 14.75 ? O2B G4P 201 A 1 HETATM 4 O O3B G4P . . . B 2 26.288 13.668 346.027 1 14.12 ? O3B G4P 201 A 1 HETATM 5 O O3A G4P . . . B 2 26.863 11.613 347.329 1 18.25 ? O3A G4P 201 A 1 HETATM 6 P PA G4P . . . B 2 27.228 11.382 348.882 1 16.69 ? PA G4P 201 A 1 HETATM 7 O O1A G4P . . . B 2 28.669 11.003 349.08 1 20.2 ? O1A G4P 201 A 1 HETATM 8 O O2A G4P . . . B 2 26.882 12.619 349.653 1 15.16 ? O2A G4P 201 A 1 HETATM 9 O O5' G4P . . . B 2 26.329 10.13 349.29 1 14.98 ? O5' G4P 201 A 1 HETATM 10 C C5' G4P . . . B 2 24.884 10.22 349.287 1 21.49 ? C5' G4P 201 A 1 HETATM 11 C C4' G4P . . . B 2 24.317 9.357 350.206 1 20.73 ? C4' G4P 201 A 1 HETATM 12 O O4' G4P . . . B 2 24.569 7.92 349.837 1 18.47 ? O4' G4P 201 A 1 HETATM 13 C C3' G4P . . . B 2 24.924 9.51 351.71 1 18.99 ? C3' G4P 201 A 1 HETATM 14 O O3' G4P . . . B 2 23.774 9.335 352.656 1 28.46 ? O3' G4P 201 A 1 HETATM 15 C C2' G4P . . . B 2 25.756 8.576 351.789 1 21.17 ? C2' G4P 201 A 1 HETATM 16 O O2' G4P . . . B 2 25.966 8.041 353.147 1 17.96 ? O2' G4P 201 A 1 HETATM 17 C C1' G4P . . . B 2 25.147 7.351 350.876 1 16.59 ? C1' G4P 201 A 1 HETATM 18 N N9 G4P . . . B 2 26.135 6.475 350.428 1 18.69 ? N9 G4P 201 A 1 HETATM 19 C C8 G4P . . . B 2 27.328 6.716 349.826 1 16.75 ? C8 G4P 201 A 1 HETATM 20 N N7 G4P . . . B 2 27.9 5.506 349.551 1 16.43 ? N7 G4P 201 A 1 HETATM 21 C C5 G4P . . . B 2 27.058 4.535 349.982 1 18.17 ? C5 G4P 201 A 1 HETATM 22 C C6 G4P . . . B 2 27.138 3.027 349.969 1 19.78 ? C6 G4P 201 A 1 HETATM 23 O O6 G4P . . . B 2 28.091 2.435 349.516 1 16.78 ? O6 G4P 201 A 1 HETATM 24 N N1 G4P . . . B 2 26.067 2.288 350.51 1 17.99 ? N1 G4P 201 A 1 HETATM 25 C C2 G4P . . . B 2 24.942 2.942 351.052 1 16.07 ? C2 G4P 201 A 1 HETATM 26 N N2 G4P . . . B 2 23.888 2.167 351.58 1 15 ? N2 G4P 201 A 1 HETATM 27 N N3 G4P . . . B 2 24.861 4.376 351.082 1 15.71 ? N3 G4P 201 A 1 HETATM 28 C C4 G4P . . . B 2 25.958 5.152 350.521 1 17.15 ? C4 G4P 201 A 1 HETATM 29 P PC G4P . . . B 2 22.875 10.56 353.17 1 41.07 ? PC G4P 201 A 1 HETATM 30 O O1C G4P . . . B 2 21.508 10.003 353.535 1 47.44 ? O1C G4P 201 A 1 HETATM 31 O O2C G4P . . . B 2 22.693 11.623 352.11 1 48.16 ? O2C G4P 201 A 1 HETATM 32 O O3C G4P . . . B 2 23.558 11.217 354.432 1 60.1 ? O3C G4P 201 A 1 HETATM 33 P PD G4P . . . B 2 24.004 10.422 355.702 1 85.4 ? PD G4P 201 A 1 HETATM 34 O O1D G4P . . . B 2 25.435 10.775 356.023 1 88.05 ? O1D G4P 201 A 1 HETATM 35 O O2D G4P . . . B 2 23.886 8.933 355.46 1 88.03 ? O2D G4P 201 A 1 HETATM 36 O O3D G4P . . . B 2 23.114 10.797 356.869 1 88.06 ? O3D G4P 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #