data_4XPD # _model_server_result.job_id LFpeXaV4lwPEa4I_OVZjyQ _model_server_result.datetime_utc '2024-11-23 11:05:28' _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 4xpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 4XPD # _exptl.entry_id 4XPD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 603.16 _entity.id 5 _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 90 _cell.angle_gamma 90 _cell.entry_id 4XPD _cell.length_a 85.564 _cell.length_b 113.649 _cell.length_c 146.721 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id D _struct_conn.ptnr1_label_atom_id N _struct_conn.ptnr1_label_comp_id SER _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_auth_asym_id F _struct_conn.ptnr1_auth_comp_id SER _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id G _struct_conn.ptnr2_label_atom_id C2 _struct_conn.ptnr2_label_comp_id CMC _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id F _struct_conn.ptnr2_auth_comp_id CMC _struct_conn.ptnr2_auth_seq_id 101 _struct_conn.ptnr2_symmetry 1_555 _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 1.325 _struct_conn.pdbx_value_order ? # _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 266 n n PB O2B G4P sing 267 n n PB O3B G4P sing 268 n n PB O3A G4P sing 269 n n O2B HOB2 G4P sing 270 n n O3B HOB3 G4P sing 271 n n O3A PA G4P sing 272 n n PA O1A G4P doub 273 n n PA O2A G4P sing 274 n n PA O5' G4P sing 275 n n O2A HOA2 G4P sing 276 n n O5' C5' G4P sing 277 n n C5' C4' G4P sing 278 n n C5' H5' G4P sing 279 n n C5' "H5''" G4P sing 280 n n C4' O4' G4P sing 281 n n C4' C3' G4P sing 282 n n C4' H4' G4P sing 283 n n O4' C1' G4P sing 284 n n C3' O3' G4P sing 285 n n C3' C2' G4P sing 286 n n C3' H3' G4P sing 287 n n O3' PC G4P sing 288 n n C2' O2' G4P sing 289 n n C2' C1' G4P sing 290 n n C2' H2' G4P sing 291 n n O2' HO2' G4P sing 292 n n C1' N9 G4P sing 293 n n C1' H1' G4P sing 294 n n N9 C8 G4P sing 295 n y N9 C4 G4P sing 296 n y C8 N7 G4P doub 297 n y C8 H8 G4P sing 298 n n N7 C5 G4P sing 299 n y C5 C6 G4P sing 300 n n C5 C4 G4P doub 301 n y C6 O6 G4P doub 302 n n C6 N1 G4P sing 303 n n N1 C2 G4P sing 304 n n N1 HN1 G4P sing 305 n n C2 N2 G4P sing 306 n n C2 N3 G4P doub 307 n n N2 HN21 G4P sing 308 n n N2 HN22 G4P sing 309 n n N3 C4 G4P sing 310 n n PC O1C G4P doub 311 n n PC O2C G4P sing 312 n n PC O3C G4P sing 313 n n O2C H2C G4P sing 314 n n O3C PD G4P sing 315 n n PD O1D G4P doub 316 n n PD O2D G4P sing 317 n n PD O3D G4P sing 318 n n O2D H2D G4P sing 319 n n O3D H3D G4P sing 320 n n # _atom_sites.entry_id 4XPD _atom_sites.fract_transf_matrix[1][1] 0.011687 _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] 0.008799 _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] 0.006816 _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 E 5 G4P A 1 901 1 G4P G4P . F 6 ACO C 1 201 1 ACO BCO . G 7 CMC F 1 101 1 CMC ACO . H 8 HOH A 1 1001 1 HOH HOH . H 8 HOH A 2 1002 2 HOH HOH . H 8 HOH A 3 1003 3 HOH HOH . H 8 HOH A 4 1004 6 HOH HOH . H 8 HOH A 5 1005 7 HOH HOH . H 8 HOH A 6 1006 8 HOH HOH . H 8 HOH A 7 1007 9 HOH HOH . H 8 HOH A 8 1008 10 HOH HOH . H 8 HOH A 9 1009 11 HOH HOH . I 8 HOH B 1 301 4 HOH HOH . I 8 HOH B 2 302 5 HOH HOH . I 8 HOH B 3 303 12 HOH HOH . J 8 HOH C 1 301 13 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 . . . E 5 21.267 -3.285 -7.415 1 82.86 ? PB G4P 901 A 1 HETATM 2 O O1B G4P . . . E 5 22.744 -3.299 -7.714 1 84.23 ? O1B G4P 901 A 1 HETATM 3 O O2B G4P . . . E 5 20.373 -3.442 -8.624 1 82.15 -1 O2B G4P 901 A 1 HETATM 4 O O3B G4P . . . E 5 20.862 -2.155 -6.497 1 80.45 ? O3B G4P 901 A 1 HETATM 5 O O3A G4P . . . E 5 21.039 -4.63 -6.54 1 91 ? O3A G4P 901 A 1 HETATM 6 P PA G4P . . . E 5 21.174 -6.139 -7.12 1 98.04 ? PA G4P 901 A 1 HETATM 7 O O1A G4P . . . E 5 19.925 -6.449 -7.916 1 100.2 -1 O1A G4P 901 A 1 HETATM 8 O O2A G4P . . . E 5 22.528 -6.286 -7.772 1 97.58 ? O2A G4P 901 A 1 HETATM 9 O O5' G4P . . . E 5 21.177 -7.07 -5.791 1 101.14 ? O5' G4P 901 A 1 HETATM 10 C C5' G4P . . . E 5 20.99 -8.493 -5.828 1 102.23 ? C5' G4P 901 A 1 HETATM 11 C C4' G4P . . . E 5 19.492 -8.818 -5.828 1 103.04 ? C4' G4P 901 A 1 HETATM 12 O O4' G4P . . . E 5 19.1 -9.726 -6.873 1 104.77 ? O4' G4P 901 A 1 HETATM 13 C C3' G4P . . . E 5 18.969 -9.445 -4.535 1 101.61 ? C3' G4P 901 A 1 HETATM 14 O O3' G4P . . . E 5 18.06 -8.543 -3.917 1 97.08 ? O3' G4P 901 A 1 HETATM 15 C C2' G4P . . . E 5 18.201 -10.677 -4.976 1 103.43 ? C2' G4P 901 A 1 HETATM 16 O O2' G4P . . . E 5 17.035 -10.906 -4.175 1 103.41 ? O2' G4P 901 A 1 HETATM 17 C C1' G4P . . . E 5 17.865 -10.287 -6.408 1 105.51 ? C1' G4P 901 A 1 HETATM 18 N N9 G4P . . . E 5 17.275 -11.374 -7.249 1 106.17 ? N9 G4P 901 A 1 HETATM 19 C C8 G4P . . . E 5 15.978 -11.729 -7.153 1 104.58 ? C8 G4P 901 A 1 HETATM 20 N N7 G4P . . . E 5 15.676 -12.715 -8.031 1 106.1 ? N7 G4P 901 A 1 HETATM 21 C C5 G4P . . . E 5 16.79 -13.006 -8.723 1 107.21 ? C5 G4P 901 A 1 HETATM 22 C C6 G4P . . . E 5 17.148 -13.959 -9.805 1 107.81 ? C6 G4P 901 A 1 HETATM 23 O O6 G4P . . . E 5 16.299 -14.743 -10.283 1 106.68 ? O6 G4P 901 A 1 HETATM 24 N N1 G4P . . . E 5 18.409 -13.959 -10.26 1 109.25 ? N1 G4P 901 A 1 HETATM 25 C C2 G4P . . . E 5 19.347 -13.123 -9.762 1 109.14 ? C2 G4P 901 A 1 HETATM 26 N N2 G4P . . . E 5 20.6 -13.188 -10.279 1 107.53 ? N2 G4P 901 A 1 HETATM 27 N N3 G4P . . . E 5 19.088 -12.223 -8.766 1 109.4 ? N3 G4P 901 A 1 HETATM 28 C C4 G4P . . . E 5 17.85 -12.116 -8.212 1 107.48 ? C4 G4P 901 A 1 HETATM 29 P PC G4P . . . E 5 18.457 -7.552 -2.715 1 93.79 ? PC G4P 901 A 1 HETATM 30 O O1C G4P . . . E 5 18.867 -8.403 -1.533 1 90.94 -1 O1C G4P 901 A 1 HETATM 31 O O2C G4P . . . E 5 17.294 -6.596 -2.581 1 93.76 ? O2C G4P 901 A 1 HETATM 32 O O3C G4P . . . E 5 19.733 -6.72 -3.265 1 86.81 ? O3C G4P 901 A 1 HETATM 33 P PD G4P . . . E 5 20.531 -5.598 -2.406 1 79.6 ? PD G4P 901 A 1 HETATM 34 O O1D G4P . . . E 5 21.348 -4.876 -3.443 1 81 ? O1D G4P 901 A 1 HETATM 35 O O2D G4P . . . E 5 19.485 -4.716 -1.773 1 80.63 -1 O2D G4P 901 A 1 HETATM 36 O O3D G4P . . . E 5 21.358 -6.384 -1.42 1 78.38 ? O3D G4P 901 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 36 #