data_3C2V # _model_server_result.job_id pFPAaA78g6Y0TLYn941lqg _model_server_result.datetime_utc '2024-10-27 22:28:33' _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 3c2v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 3C2V # _exptl.entry_id 3C2V _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 3C2V _cell.length_a 154.668 _cell.length_b 154.668 _cell.length_c 69.346 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C2V _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,D _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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 69.346 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' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 69.346 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' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 69.346 # _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 295 n n C1 O1 PRP sing 296 n n C1 O4 PRP sing 297 n n C1 H1 PRP sing 298 n n C2 C3 PRP sing 299 n n C2 O2 PRP sing 300 n n C2 H2 PRP sing 301 n n C3 C4 PRP sing 302 n n C3 O3 PRP sing 303 n n C3 H3 PRP sing 304 n n C4 C5 PRP sing 305 n n C4 O4 PRP sing 306 n n C4 H4 PRP sing 307 n n C5 O5 PRP sing 308 n n C5 H51 PRP sing 309 n n C5 H52 PRP sing 310 n n O1 PA PRP sing 311 n n O2 HO2 PRP sing 312 n n O3 HO3 PRP sing 313 n n O5 P PRP sing 314 n n P O1P PRP doub 315 n n P O2P PRP sing 316 n n P O3P PRP sing 317 n n O2P HOP2 PRP sing 318 n n O3P HOP3 PRP sing 319 n n PA O1A PRP doub 320 n n PA O2A PRP sing 321 n n PA O3A PRP sing 322 n n O2A HOA2 PRP sing 323 n n O3A PB PRP sing 324 n n PB O1B PRP doub 325 n n PB O2B PRP sing 326 n n PB O3B PRP sing 327 n n O2B HOB2 PRP sing 328 n n O3B HOB3 PRP sing 329 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 3C2V _atom_sites.fract_transf_matrix[1][1] 0.006465 _atom_sites.fract_transf_matrix[1][2] 0.003733 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007466 _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] 0.01442 _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 PHT A 1 301 301 PHT PHT . D 4 HOH A 1 302 302 HOH HOH . D 4 HOH A 2 303 303 HOH HOH . D 4 HOH A 3 304 304 HOH HOH . D 4 HOH A 4 305 305 HOH HOH . D 4 HOH A 5 306 306 HOH HOH . D 4 HOH A 6 307 307 HOH HOH . D 4 HOH A 7 308 308 HOH HOH . D 4 HOH A 8 309 309 HOH HOH . D 4 HOH A 9 310 310 HOH HOH . D 4 HOH A 10 311 311 HOH HOH . D 4 HOH A 11 312 312 HOH HOH . D 4 HOH A 12 313 313 HOH HOH . D 4 HOH A 13 314 314 HOH HOH . D 4 HOH A 14 315 315 HOH HOH . D 4 HOH A 15 316 316 HOH HOH . D 4 HOH A 16 317 317 HOH HOH . D 4 HOH A 17 319 319 HOH HOH . D 4 HOH A 18 320 320 HOH HOH . D 4 HOH A 19 321 321 HOH HOH . D 4 HOH A 20 322 322 HOH HOH . D 4 HOH A 21 323 323 HOH HOH . D 4 HOH A 22 324 324 HOH HOH . D 4 HOH A 23 325 325 HOH HOH . D 4 HOH A 24 326 326 HOH HOH . D 4 HOH A 25 327 327 HOH HOH . D 4 HOH A 26 328 328 HOH HOH . D 4 HOH A 27 329 329 HOH HOH . D 4 HOH A 28 330 330 HOH HOH . D 4 HOH A 29 331 331 HOH HOH . D 4 HOH A 30 332 332 HOH HOH . D 4 HOH A 31 333 333 HOH HOH . D 4 HOH A 32 334 334 HOH HOH . D 4 HOH A 33 335 335 HOH HOH . D 4 HOH A 34 336 336 HOH HOH . D 4 HOH A 35 337 337 HOH HOH . D 4 HOH A 36 338 338 HOH HOH . D 4 HOH A 37 339 339 HOH HOH . D 4 HOH A 38 340 340 HOH HOH . D 4 HOH A 39 341 341 HOH HOH . D 4 HOH A 40 342 342 HOH HOH . D 4 HOH A 41 343 343 HOH HOH . D 4 HOH A 42 344 344 HOH HOH . D 4 HOH A 43 345 345 HOH HOH . D 4 HOH A 44 346 346 HOH HOH . D 4 HOH A 45 347 347 HOH HOH . D 4 HOH A 46 348 348 HOH HOH . D 4 HOH A 47 349 349 HOH HOH . D 4 HOH A 48 350 350 HOH HOH . D 4 HOH A 49 351 351 HOH HOH . D 4 HOH A 50 352 352 HOH HOH . D 4 HOH A 51 353 353 HOH HOH . D 4 HOH A 52 354 354 HOH HOH . D 4 HOH A 53 355 355 HOH HOH . D 4 HOH A 54 356 356 HOH HOH . D 4 HOH A 55 357 357 HOH HOH . D 4 HOH A 56 358 358 HOH HOH . D 4 HOH A 57 359 359 HOH HOH . D 4 HOH A 58 360 360 HOH HOH . D 4 HOH A 59 361 361 HOH HOH . D 4 HOH A 60 362 362 HOH HOH . D 4 HOH A 61 363 363 HOH HOH . D 4 HOH A 62 364 364 HOH HOH . D 4 HOH A 63 365 365 HOH HOH . D 4 HOH A 64 366 366 HOH HOH . D 4 HOH A 65 367 367 HOH HOH . D 4 HOH A 66 368 368 HOH HOH . D 4 HOH A 67 369 369 HOH HOH . D 4 HOH A 68 370 370 HOH HOH . D 4 HOH A 69 371 371 HOH HOH . D 4 HOH A 70 372 372 HOH HOH . D 4 HOH A 71 373 373 HOH HOH . D 4 HOH A 72 374 374 HOH HOH . D 4 HOH A 73 375 375 HOH HOH . D 4 HOH A 74 376 376 HOH HOH . D 4 HOH A 75 377 377 HOH HOH . D 4 HOH A 76 378 378 HOH HOH . D 4 HOH A 77 379 379 HOH HOH . D 4 HOH A 78 380 380 HOH HOH . D 4 HOH A 79 381 381 HOH HOH . D 4 HOH A 80 382 382 HOH HOH . D 4 HOH A 81 383 383 HOH HOH . D 4 HOH A 82 384 384 HOH HOH . D 4 HOH A 83 385 385 HOH HOH . D 4 HOH A 84 386 386 HOH HOH . D 4 HOH A 85 387 387 HOH HOH . D 4 HOH A 86 388 388 HOH HOH . D 4 HOH A 87 389 389 HOH HOH . D 4 HOH A 88 390 390 HOH HOH . D 4 HOH A 89 391 391 HOH HOH . D 4 HOH A 90 392 392 HOH HOH . D 4 HOH A 91 393 393 HOH HOH . D 4 HOH A 92 394 394 HOH HOH . D 4 HOH A 93 395 395 HOH HOH . D 4 HOH A 94 396 396 HOH HOH . D 4 HOH A 95 397 397 HOH HOH . D 4 HOH A 96 398 398 HOH HOH . D 4 HOH A 97 399 399 HOH HOH . D 4 HOH A 98 400 400 HOH HOH . D 4 HOH A 99 401 401 HOH HOH . D 4 HOH A 100 402 402 HOH HOH . D 4 HOH A 101 403 403 HOH HOH . D 4 HOH A 102 404 404 HOH HOH . D 4 HOH A 103 405 405 HOH HOH . D 4 HOH A 104 406 406 HOH HOH . D 4 HOH A 105 407 407 HOH HOH . D 4 HOH A 106 408 408 HOH HOH . D 4 HOH A 107 409 409 HOH HOH . D 4 HOH A 108 410 410 HOH HOH . D 4 HOH A 109 411 411 HOH HOH . D 4 HOH A 110 412 412 HOH HOH . D 4 HOH A 111 413 413 HOH HOH . D 4 HOH A 112 414 414 HOH HOH . D 4 HOH A 113 415 415 HOH HOH . D 4 HOH A 114 416 416 HOH HOH . D 4 HOH A 115 417 417 HOH HOH . D 4 HOH A 116 418 418 HOH HOH . D 4 HOH A 117 419 419 HOH HOH . D 4 HOH A 118 420 420 HOH HOH . D 4 HOH A 119 421 421 HOH HOH . D 4 HOH A 120 422 422 HOH HOH . D 4 HOH A 121 423 423 HOH HOH . D 4 HOH A 122 424 424 HOH HOH . D 4 HOH A 123 425 425 HOH HOH . D 4 HOH A 124 426 426 HOH HOH . D 4 HOH A 125 427 427 HOH HOH . D 4 HOH A 126 428 428 HOH HOH . D 4 HOH A 127 429 429 HOH HOH . D 4 HOH A 128 430 430 HOH HOH . D 4 HOH A 129 431 431 HOH HOH . D 4 HOH A 130 432 432 HOH HOH . D 4 HOH A 131 433 433 HOH HOH . D 4 HOH A 132 434 434 HOH HOH . D 4 HOH A 133 435 435 HOH HOH . D 4 HOH A 134 436 436 HOH HOH . D 4 HOH A 135 437 437 HOH HOH . D 4 HOH A 136 438 438 HOH HOH . D 4 HOH A 137 439 439 HOH HOH . D 4 HOH A 138 440 440 HOH HOH . D 4 HOH A 139 441 441 HOH HOH . D 4 HOH A 140 442 442 HOH HOH . D 4 HOH A 141 443 443 HOH HOH . D 4 HOH A 142 445 445 HOH HOH . D 4 HOH A 143 446 446 HOH HOH . D 4 HOH A 144 447 447 HOH HOH . D 4 HOH A 145 448 448 HOH HOH . D 4 HOH A 146 449 449 HOH HOH . D 4 HOH A 147 450 450 HOH HOH . D 4 HOH A 148 451 451 HOH HOH . D 4 HOH A 149 452 452 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 -26.255 -16.432 44.971 1 105.3 ? C1 PRP 300 A 1 HETATM 2 C C2 PRP . . . B 2 -27.61 -15.888 44.484 1 78.38 ? C2 PRP 300 A 1 HETATM 3 C C3 PRP . . . B 2 -28.298 -17.101 43.954 1 76.15 ? C3 PRP 300 A 1 HETATM 4 C C4 PRP . . . B 2 -27.211 -18.089 43.608 1 89.99 ? C4 PRP 300 A 1 HETATM 5 C C5 PRP . . . B 2 -27.14 -18.259 42.094 1 45.54 ? C5 PRP 300 A 1 HETATM 6 O O1 PRP . . . B 2 -26.21 -16.758 46.358 1 104.1 ? O1 PRP 300 A 1 HETATM 7 O O2 PRP . . . B 2 -28.471 -15.273 45.447 1 54.07 ? O2 PRP 300 A 1 HETATM 8 O O3 PRP . . . B 2 -29.14 -17.659 44.96 1 75.45 ? O3 PRP 300 A 1 HETATM 9 O O4 PRP . . . B 2 -26.005 -17.597 44.199 1 95.45 ? O4 PRP 300 A 1 HETATM 10 O O5 PRP . . . B 2 -26.011 -18.975 41.701 1 54.71 ? O5 PRP 300 A 1 HETATM 11 P P PRP . . . B 2 -25.957 -20.543 41.501 1 106.56 ? P PRP 300 A 1 HETATM 12 O O1P PRP . . . B 2 -24.431 -20.636 41.522 1 62.65 ? O1P PRP 300 A 1 HETATM 13 O O2P PRP . . . B 2 -26.572 -21.12 42.746 1 60.52 ? O2P PRP 300 A 1 HETATM 14 O O3P PRP . . . B 2 -26.621 -20.797 40.25 1 34 ? O3P PRP 300 A 1 HETATM 15 P PA PRP . . . B 2 -24.93 -17.346 47.142 1 115.47 ? PA PRP 300 A 1 HETATM 16 O O1A PRP . . . B 2 -25.458 -17.657 48.501 1 52.53 ? O1A PRP 300 A 1 HETATM 17 O O2A PRP . . . B 2 -24.352 -18.422 46.275 1 39.96 ? O2A PRP 300 A 1 HETATM 18 O O3A PRP . . . B 2 -23.768 -15.961 47.302 1 109.27 ? O3A PRP 300 A 1 HETATM 19 P PB PRP . . . B 2 -22.217 -16.243 48.216 1 161.19 ? PB PRP 300 A 1 HETATM 20 O O1B PRP . . . B 2 -21.663 -17.426 47.474 1 59.48 ? O1B PRP 300 A 1 HETATM 21 O O2B PRP . . . B 2 -21.366 -15.034 48.054 1 160.65 ? O2B PRP 300 A 1 HETATM 22 O O3B PRP . . . B 2 -22.482 -16.169 49.687 1 66.5 ? O3B PRP 300 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #