data_5HKF # _model_server_result.job_id a5p8oG_4s7FjRJCvUSY5Dg _model_server_result.datetime_utc '2024-10-10 00:25:51' _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 5hkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 5HKF # _exptl.entry_id 5HKF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.07 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.86 _cell.angle_gamma 90 _cell.entry_id 5HKF _cell.length_a 56.201 _cell.length_b 58.629 _cell.length_c 57.224 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C5 H13 O14 P3' _chem_comp.formula_weight 390.07 _chem_comp.id PRP _chem_comp.mon_nstd_flag n _chem_comp.name 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID;1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose;1-O-pyrophosphono-5-O-phosphono-D-ribose;1-O-pyrophosphono-5-O-phosphono-ribose' # 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 C1 C2 PRP sing 264 n n C1 O1 PRP sing 265 n n C1 O4 PRP sing 266 n n C1 H1 PRP sing 267 n n C2 C3 PRP sing 268 n n C2 O2 PRP sing 269 n n C2 H2 PRP sing 270 n n C3 C4 PRP sing 271 n n C3 O3 PRP sing 272 n n C3 H3 PRP sing 273 n n C4 C5 PRP sing 274 n n C4 O4 PRP sing 275 n n C4 H4 PRP sing 276 n n C5 O5 PRP sing 277 n n C5 H51 PRP sing 278 n n C5 H52 PRP sing 279 n n O1 PA PRP sing 280 n n O2 HO2 PRP sing 281 n n O3 HO3 PRP sing 282 n n O5 P PRP sing 283 n n P O1P PRP doub 284 n n P O2P PRP sing 285 n n P O3P PRP sing 286 n n O2P HOP2 PRP sing 287 n n O3P HOP3 PRP sing 288 n n PA O1A PRP doub 289 n n PA O2A PRP sing 290 n n PA O3A PRP sing 291 n n O2A HOA2 PRP sing 292 n n O3A PB PRP sing 293 n n PB O1B PRP doub 294 n n PB O2B PRP sing 295 n n PB O3B PRP sing 296 n n O2B HOB2 PRP sing 297 n n O3B HOB3 PRP sing 298 n n # _pdbx_chem_comp_identifier.comp_id PRP _pdbx_chem_comp_identifier.identifier a-D-Ribf1PO35PO3 _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 5HKF _atom_sites.fract_transf_matrix[1][1] 0.017793 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.009013 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017056 _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] 0.019589 _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 2 PRP A 1 201 179 PRP PRP . D 2 PRP B 1 201 178 PRP PRP . E 3 HOH A 1 301 15 HOH HOH . E 3 HOH A 2 302 63 HOH HOH . E 3 HOH A 3 303 73 HOH HOH . E 3 HOH A 4 304 23 HOH HOH . E 3 HOH A 5 305 85 HOH HOH . E 3 HOH A 6 306 12 HOH HOH . E 3 HOH A 7 307 37 HOH HOH . E 3 HOH A 8 308 27 HOH HOH . E 3 HOH A 9 309 4 HOH HOH . E 3 HOH A 10 310 58 HOH HOH . E 3 HOH A 11 311 43 HOH HOH . E 3 HOH A 12 312 21 HOH HOH . E 3 HOH A 13 313 71 HOH HOH . E 3 HOH A 14 314 81 HOH HOH . E 3 HOH A 15 315 82 HOH HOH . E 3 HOH A 16 316 22 HOH HOH . E 3 HOH A 17 317 42 HOH HOH . E 3 HOH A 18 318 47 HOH HOH . E 3 HOH A 19 319 31 HOH HOH . E 3 HOH A 20 320 70 HOH HOH . E 3 HOH A 21 321 66 HOH HOH . E 3 HOH A 22 322 87 HOH HOH . E 3 HOH A 23 323 72 HOH HOH . E 3 HOH A 24 324 32 HOH HOH . E 3 HOH A 25 325 83 HOH HOH . E 3 HOH A 26 326 84 HOH HOH . E 3 HOH A 27 327 56 HOH HOH . E 3 HOH A 28 328 38 HOH HOH . E 3 HOH A 29 329 54 HOH HOH . F 3 HOH B 1 301 20 HOH HOH . F 3 HOH B 2 302 44 HOH HOH . F 3 HOH B 3 303 2 HOH HOH . F 3 HOH B 4 304 16 HOH HOH . F 3 HOH B 5 305 1 HOH HOH . F 3 HOH B 6 306 53 HOH HOH . F 3 HOH B 7 307 6 HOH HOH . F 3 HOH B 8 308 13 HOH HOH . F 3 HOH B 9 309 3 HOH HOH . F 3 HOH B 10 310 69 HOH HOH . F 3 HOH B 11 311 5 HOH HOH . F 3 HOH B 12 312 79 HOH HOH . F 3 HOH B 13 313 29 HOH HOH . F 3 HOH B 14 314 40 HOH HOH . F 3 HOH B 15 315 30 HOH HOH . F 3 HOH B 16 316 26 HOH HOH . F 3 HOH B 17 317 10 HOH HOH . F 3 HOH B 18 318 41 HOH HOH . F 3 HOH B 19 319 17 HOH HOH . F 3 HOH B 20 320 7 HOH HOH . F 3 HOH B 21 321 77 HOH HOH . F 3 HOH B 22 322 60 HOH HOH . F 3 HOH B 23 323 57 HOH HOH . F 3 HOH B 24 324 80 HOH HOH . F 3 HOH B 25 325 48 HOH HOH . F 3 HOH B 26 326 28 HOH HOH . F 3 HOH B 27 327 74 HOH HOH . F 3 HOH B 28 328 9 HOH HOH . F 3 HOH B 29 329 50 HOH HOH . F 3 HOH B 30 330 34 HOH HOH . F 3 HOH B 31 331 8 HOH HOH . F 3 HOH B 32 332 11 HOH HOH . F 3 HOH B 33 333 45 HOH HOH . F 3 HOH B 34 334 14 HOH HOH . F 3 HOH B 35 335 36 HOH HOH . F 3 HOH B 36 336 18 HOH HOH . F 3 HOH B 37 337 39 HOH HOH . F 3 HOH B 38 338 24 HOH HOH . F 3 HOH B 39 339 49 HOH HOH . F 3 HOH B 40 340 35 HOH HOH . F 3 HOH B 41 341 65 HOH HOH . F 3 HOH B 42 342 86 HOH HOH . F 3 HOH B 43 343 55 HOH HOH . F 3 HOH B 44 344 25 HOH HOH . F 3 HOH B 45 345 68 HOH HOH . F 3 HOH B 46 346 64 HOH HOH . F 3 HOH B 47 347 33 HOH HOH . F 3 HOH B 48 348 19 HOH HOH . F 3 HOH B 49 349 51 HOH HOH . F 3 HOH B 50 350 61 HOH HOH . F 3 HOH B 51 351 62 HOH HOH . F 3 HOH B 52 352 76 HOH HOH . F 3 HOH B 53 353 46 HOH HOH . F 3 HOH B 54 354 52 HOH HOH . F 3 HOH B 55 355 78 HOH HOH . F 3 HOH B 56 356 75 HOH HOH . F 3 HOH B 57 357 59 HOH HOH . F 3 HOH B 58 358 67 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 C C1 PRP . . . D 2 50.516 11.493 45.844 1 84.17 ? C1 PRP 201 B 1 HETATM 2 C C2 PRP . . . D 2 50.483 10.043 45.358 1 79.47 ? C2 PRP 201 B 1 HETATM 3 C C3 PRP . . . D 2 51.918 9.572 45.523 1 77.44 ? C3 PRP 201 B 1 HETATM 4 C C4 PRP . . . D 2 52.776 10.837 45.633 1 68.98 ? C4 PRP 201 B 1 HETATM 5 C C5 PRP . . . D 2 53.889 11.014 44.594 1 58.96 ? C5 PRP 201 B 1 HETATM 6 O O1 PRP . . . D 2 50.181 11.574 47.252 1 98.54 ? O1 PRP 201 B 1 HETATM 7 O O2 PRP . . . D 2 49.578 9.21 46.099 1 77.67 ? O2 PRP 201 B 1 HETATM 8 O O3 PRP . . . D 2 52.03 8.777 46.713 1 69.72 ? O3 PRP 201 B 1 HETATM 9 O O4 PRP . . . D 2 51.856 11.936 45.566 1 77.72 ? O4 PRP 201 B 1 HETATM 10 O O5 PRP . . . D 2 54.96 11.633 45.302 1 46.54 ? O5 PRP 201 B 1 HETATM 11 P P PRP . . . D 2 56.497 11.754 44.883 1 42.57 ? P PRP 201 B 1 HETATM 12 O O1P PRP . . . D 2 56.835 10.57 43.981 1 38.57 ? O1P PRP 201 B 1 HETATM 13 O O2P PRP . . . D 2 57.132 11.766 46.241 1 38.07 ? O2P PRP 201 B 1 HETATM 14 O O3P PRP . . . D 2 56.686 13.091 44.186 1 41.12 ? O3P PRP 201 B 1 HETATM 15 P PA PRP . . . D 2 50.303 12.856 48.28 1 107.19 ? PA PRP 201 B 1 HETATM 16 O O1A PRP . . . D 2 49.525 14.034 47.724 1 92.99 ? O1A PRP 201 B 1 HETATM 17 O O2A PRP . . . D 2 51.77 13.096 48.583 1 102.95 ? O2A PRP 201 B 1 HETATM 18 O O3A PRP . . . D 2 49.506 12.366 49.643 1 96.21 ? O3A PRP 201 B 1 HETATM 19 P PB PRP . . . D 2 49.998 11.357 50.836 1 76.62 ? PB PRP 201 B 1 HETATM 20 O O1B PRP . . . D 2 50.016 9.964 50.257 1 74.31 ? O1B PRP 201 B 1 HETATM 21 O O2B PRP . . . D 2 51.385 11.81 51.209 1 91.9 ? O2B PRP 201 B 1 HETATM 22 O O3B PRP . . . D 2 48.974 11.574 51.925 1 86.81 ? O3B PRP 201 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #