data_3C2F # _model_server_result.job_id V6TKW4v3IROsQiubTRfFWQ _model_server_result.datetime_utc '2024-10-27 22:34:35' _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 3c2f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 3C2F # _exptl.entry_id 3C2F _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 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 3C2F _cell.length_a 154.905 _cell.length_b 154.905 _cell.length_c 70.57 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C2F _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_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 1,2,3,4,5,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 70.57 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 70.57 5 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 70.57 # _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 '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 277 n n C1 O1 PRP sing 278 n n C1 O4 PRP sing 279 n n C1 H1 PRP sing 280 n n C2 C3 PRP sing 281 n n C2 O2 PRP sing 282 n n C2 H2 PRP sing 283 n n C3 C4 PRP sing 284 n n C3 O3 PRP sing 285 n n C3 H3 PRP sing 286 n n C4 C5 PRP sing 287 n n C4 O4 PRP sing 288 n n C4 H4 PRP sing 289 n n C5 O5 PRP sing 290 n n C5 H51 PRP sing 291 n n C5 H52 PRP sing 292 n n O1 PA PRP sing 293 n n O2 HO2 PRP sing 294 n n O3 HO3 PRP sing 295 n n O5 P PRP sing 296 n n P O1P PRP doub 297 n n P O2P PRP sing 298 n n P O3P PRP sing 299 n n O2P HOP2 PRP sing 300 n n O3P HOP3 PRP sing 301 n n PA O1A PRP doub 302 n n PA O2A PRP sing 303 n n PA O3A PRP sing 304 n n O2A HOA2 PRP sing 305 n n O3A PB PRP sing 306 n n PB O1B PRP doub 307 n n PB O2B PRP sing 308 n n PB O3B PRP sing 309 n n O2B HOB2 PRP sing 310 n n O3B HOB3 PRP sing 311 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 3C2F _atom_sites.fract_transf_matrix[1][1] 0.006456 _atom_sites.fract_transf_matrix[1][2] 0.003727 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007454 _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] 0.01417 _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 PRP A 1 300 300 PRP PRP . C 3 HOH A 1 301 301 HOH HOH . C 3 HOH A 2 302 302 HOH HOH . C 3 HOH A 3 303 303 HOH HOH . C 3 HOH A 4 304 304 HOH HOH . C 3 HOH A 5 305 305 HOH HOH . C 3 HOH A 6 306 306 HOH HOH . C 3 HOH A 7 307 307 HOH HOH . C 3 HOH A 8 308 308 HOH HOH . C 3 HOH A 9 309 309 HOH HOH . C 3 HOH A 10 310 310 HOH HOH . C 3 HOH A 11 311 311 HOH HOH . C 3 HOH A 12 312 312 HOH HOH . C 3 HOH A 13 313 313 HOH HOH . C 3 HOH A 14 314 314 HOH HOH . C 3 HOH A 15 315 315 HOH HOH . C 3 HOH A 16 316 316 HOH HOH . C 3 HOH A 17 317 317 HOH HOH . C 3 HOH A 18 318 318 HOH HOH . C 3 HOH A 19 319 319 HOH HOH . C 3 HOH A 20 320 320 HOH HOH . C 3 HOH A 21 321 321 HOH HOH . C 3 HOH A 22 322 322 HOH HOH . C 3 HOH A 23 324 324 HOH HOH . C 3 HOH A 24 325 325 HOH HOH . C 3 HOH A 25 326 326 HOH HOH . C 3 HOH A 26 327 327 HOH HOH . C 3 HOH A 27 328 328 HOH HOH . C 3 HOH A 28 329 329 HOH HOH . C 3 HOH A 29 330 330 HOH HOH . C 3 HOH A 30 331 331 HOH HOH . C 3 HOH A 31 333 333 HOH HOH . C 3 HOH A 32 334 334 HOH HOH . C 3 HOH A 33 335 335 HOH HOH . C 3 HOH A 34 336 336 HOH HOH . C 3 HOH A 35 337 337 HOH HOH . C 3 HOH A 36 338 338 HOH HOH . C 3 HOH A 37 339 339 HOH HOH . C 3 HOH A 38 340 340 HOH HOH . C 3 HOH A 39 341 341 HOH HOH . C 3 HOH A 40 342 342 HOH HOH . C 3 HOH A 41 343 343 HOH HOH . C 3 HOH A 42 344 344 HOH HOH . C 3 HOH A 43 345 345 HOH HOH . C 3 HOH A 44 346 346 HOH HOH . C 3 HOH A 45 347 347 HOH HOH . C 3 HOH A 46 348 348 HOH HOH . C 3 HOH A 47 349 349 HOH HOH . C 3 HOH A 48 350 350 HOH HOH . C 3 HOH A 49 351 351 HOH HOH . C 3 HOH A 50 352 352 HOH HOH . C 3 HOH A 51 353 353 HOH HOH . C 3 HOH A 52 354 354 HOH HOH . C 3 HOH A 53 355 355 HOH HOH . C 3 HOH A 54 356 356 HOH HOH . C 3 HOH A 55 357 357 HOH HOH . C 3 HOH A 56 358 358 HOH HOH . C 3 HOH A 57 359 359 HOH HOH . C 3 HOH A 58 360 360 HOH HOH . C 3 HOH A 59 361 361 HOH HOH . C 3 HOH A 60 362 362 HOH HOH . C 3 HOH A 61 363 363 HOH HOH . C 3 HOH A 62 364 364 HOH HOH . C 3 HOH A 63 365 365 HOH HOH . C 3 HOH A 64 366 366 HOH HOH . C 3 HOH A 65 367 367 HOH HOH . C 3 HOH A 66 368 368 HOH HOH . C 3 HOH A 67 369 369 HOH HOH . C 3 HOH A 68 370 370 HOH HOH . C 3 HOH A 69 371 371 HOH HOH . C 3 HOH A 70 372 372 HOH HOH . C 3 HOH A 71 373 373 HOH HOH . C 3 HOH A 72 374 374 HOH HOH . C 3 HOH A 73 375 375 HOH HOH . C 3 HOH A 74 376 376 HOH HOH . C 3 HOH A 75 377 377 HOH HOH . C 3 HOH A 76 378 378 HOH HOH . C 3 HOH A 77 379 379 HOH HOH . C 3 HOH A 78 380 380 HOH HOH . C 3 HOH A 79 381 381 HOH HOH . C 3 HOH A 80 382 382 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 . . . B 2 26.597 -14.916 44.878 1 92.8 ? C1 PRP 300 A 1 HETATM 2 C C2 PRP . . . B 2 26.531 -16.231 44.189 1 90.48 ? C2 PRP 300 A 1 HETATM 3 C C3 PRP . . . B 2 27.12 -15.808 42.893 1 84.8 ? C3 PRP 300 A 1 HETATM 4 C C4 PRP . . . B 2 28.329 -15.071 43.387 1 67.38 ? C4 PRP 300 A 1 HETATM 5 C C5 PRP . . . B 2 28.931 -14.17 42.366 1 37.75 ? C5 PRP 300 A 1 HETATM 6 O O1 PRP . . . B 2 26.682 -15.216 46.247 1 101.32 ? O1 PRP 300 A 1 HETATM 7 O O2 PRP . . . B 2 27.464 -17.006 44.905 1 64.69 ? O2 PRP 300 A 1 HETATM 8 O O3 PRP . . . B 2 27.392 -16.979 42.137 1 128.6 ? O3 PRP 300 A 1 HETATM 9 O O4 PRP . . . B 2 27.766 -14.291 44.394 1 64.84 ? O4 PRP 300 A 1 HETATM 10 O O5 PRP . . . B 2 30.134 -13.666 42.869 1 49.58 ? O5 PRP 300 A 1 HETATM 11 P P PRP . . . B 2 30.766 -12.347 42.334 1 44.61 ? P PRP 300 A 1 HETATM 12 O O1P PRP . . . B 2 29.854 -11.258 42.524 1 62.4 ? O1P PRP 300 A 1 HETATM 13 O O2P PRP . . . B 2 31.832 -12.24 43.274 1 50.59 ? O2P PRP 300 A 1 HETATM 14 O O3P PRP . . . B 2 31.114 -12.735 40.988 1 37.62 ? O3P PRP 300 A 1 HETATM 15 P PA PRP . . . B 2 25.791 -14.349 47.212 1 85.42 ? PA PRP 300 A 1 HETATM 16 O O1A PRP . . . B 2 25.136 -13.375 46.321 1 85.55 ? O1A PRP 300 A 1 HETATM 17 O O2A PRP . . . B 2 24.939 -15.263 47.985 1 78.6 ? O2A PRP 300 A 1 HETATM 18 O O3A PRP . . . B 2 27.047 -13.73 48.313 1 77.95 ? O3A PRP 300 A 1 HETATM 19 P PB PRP . . . B 2 27.751 -12.152 47.857 1 90.04 ? PB PRP 300 A 1 HETATM 20 O O1B PRP . . . B 2 26.68 -11.123 47.845 1 62.82 ? O1B PRP 300 A 1 HETATM 21 O O2B PRP . . . B 2 28.472 -12.318 46.604 1 50.84 ? O2B PRP 300 A 1 HETATM 22 O O3B PRP . . . B 2 28.661 -12.022 49.014 1 106.06 ? O3B PRP 300 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 22 #