data_5LLF # _model_server_result.job_id tMUkCXKNnJi8pTuyA2Rk_A _model_server_result.datetime_utc '2025-03-30 19:00:41' _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 5llf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":301}' # _entry.id 5LLF # _exptl.entry_id 5LLF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 497.895 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] phosphono hydrogen phosphate' _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 5LLF _cell.length_a 73.44 _cell.length_b 165.94 _cell.length_c 255.3 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LLF _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,Q,R 1 1 C,D,J,K,L,M,N,O,P,S,T 2 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 6 _struct_asym.id N _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'H8 O19 P6' _chem_comp.formula_weight 497.895 _chem_comp.id 6YW _chem_comp.mon_nstd_flag . _chem_comp.name '[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] phosphono hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O20 P17 6YW doub 1 n n P17 O18 6YW sing 2 n n P17 O16 6YW sing 3 n n P17 O19 6YW sing 4 n n O16 P14 6YW sing 5 n n O21 P14 6YW doub 6 n n P14 O15 6YW sing 7 n n P14 O13 6YW sing 8 n n O24 P05 6YW doub 9 n n O12 P11 6YW doub 10 n n O01 P02 6YW doub 11 n n O13 P11 6YW sing 12 n n O06 P05 6YW sing 13 n n P11 O10 6YW sing 14 n n P11 O22 6YW sing 15 n n O25 P02 6YW sing 16 n n P05 O04 6YW sing 17 n n P05 O07 6YW sing 18 n n O10 P08 6YW sing 19 n n P02 O04 6YW sing 20 n n P02 O03 6YW sing 21 n n O07 P08 6YW sing 22 n n P08 O09 6YW doub 23 n n P08 O23 6YW sing 24 n n O03 H1 6YW sing 25 n n O06 H2 6YW sing 26 n n O15 H3 6YW sing 27 n n O18 H4 6YW sing 28 n n O19 H5 6YW sing 29 n n O22 H6 6YW sing 30 n n O23 H7 6YW sing 31 n n O25 H8 6YW sing 32 n n # _atom_sites.entry_id 5LLF _atom_sites.fract_transf_matrix[1][1] 0.013617 _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] 0.006026 _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] 0.003917 _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 2 PO4 A 1 301 269 PO4 PO4 . F 2 PO4 A 1 302 270 PO4 PO4 . G 3 6YX A 1 303 269 6YX POL . H 2 PO4 B 1 301 270 PO4 PO4 . I 2 PO4 B 1 302 271 PO4 PO4 . J 4 6YY C 1 301 269 6YY PPL . K 5 CL C 1 302 270 CL CL . L 2 PO4 C 1 303 271 PO4 PO4 . M 2 PO4 C 1 304 272 PO4 PO4 . N 6 6YW D 1 301 270 6YW PFL . O 2 PO4 D 1 302 271 PO4 PO4 . P 2 PO4 D 1 303 272 PO4 PO4 . Q 7 HOH A 1 401 323 HOH HOH . Q 7 HOH A 2 402 316 HOH HOH . Q 7 HOH A 3 403 294 HOH HOH . Q 7 HOH A 4 404 306 HOH HOH . Q 7 HOH A 5 405 331 HOH HOH . Q 7 HOH A 6 406 305 HOH HOH . Q 7 HOH A 7 407 279 HOH HOH . Q 7 HOH A 8 408 280 HOH HOH . Q 7 HOH A 9 409 304 HOH HOH . Q 7 HOH A 10 410 301 HOH HOH . Q 7 HOH A 11 411 272 HOH HOH . Q 7 HOH A 12 412 274 HOH HOH . Q 7 HOH A 13 413 287 HOH HOH . Q 7 HOH A 14 414 283 HOH HOH . Q 7 HOH A 15 415 289 HOH HOH . Q 7 HOH A 16 416 293 HOH HOH . Q 7 HOH A 17 417 295 HOH HOH . Q 7 HOH A 18 418 300 HOH HOH . Q 7 HOH A 19 419 290 HOH HOH . Q 7 HOH A 20 420 282 HOH HOH . Q 7 HOH A 21 421 308 HOH HOH . Q 7 HOH A 22 422 318 HOH HOH . Q 7 HOH A 23 423 292 HOH HOH . Q 7 HOH A 24 424 284 HOH HOH . Q 7 HOH A 25 425 275 HOH HOH . Q 7 HOH A 26 426 296 HOH HOH . Q 7 HOH A 27 427 276 HOH HOH . Q 7 HOH A 28 428 322 HOH HOH . Q 7 HOH A 29 429 306 HOH HOH . Q 7 HOH A 30 430 281 HOH HOH . Q 7 HOH A 31 431 309 HOH HOH . Q 7 HOH A 32 432 292 HOH HOH . Q 7 HOH A 33 433 322 HOH HOH . Q 7 HOH A 34 434 277 HOH HOH . Q 7 HOH A 35 435 297 HOH HOH . Q 7 HOH A 36 436 323 HOH HOH . Q 7 HOH A 37 437 303 HOH HOH . Q 7 HOH A 38 438 299 HOH HOH . Q 7 HOH A 39 439 294 HOH HOH . Q 7 HOH A 40 440 302 HOH HOH . Q 7 HOH A 41 441 278 HOH HOH . Q 7 HOH A 42 442 285 HOH HOH . Q 7 HOH A 43 443 321 HOH HOH . Q 7 HOH A 44 444 330 HOH HOH . Q 7 HOH A 45 445 271 HOH HOH . Q 7 HOH A 46 446 288 HOH HOH . Q 7 HOH A 47 447 317 HOH HOH . Q 7 HOH A 48 448 273 HOH HOH . Q 7 HOH A 49 449 319 HOH HOH . Q 7 HOH A 50 450 308 HOH HOH . Q 7 HOH A 51 451 307 HOH HOH . Q 7 HOH A 52 452 291 HOH HOH . Q 7 HOH A 53 453 298 HOH HOH . Q 7 HOH A 54 454 320 HOH HOH . Q 7 HOH A 55 455 286 HOH HOH . Q 7 HOH A 56 456 311 HOH HOH . Q 7 HOH A 57 457 312 HOH HOH . Q 7 HOH A 58 458 310 HOH HOH . Q 7 HOH A 59 459 313 HOH HOH . Q 7 HOH A 60 460 315 HOH HOH . Q 7 HOH A 61 461 314 HOH HOH . R 7 HOH B 1 401 284 HOH HOH . R 7 HOH B 2 402 290 HOH HOH . R 7 HOH B 3 403 302 HOH HOH . R 7 HOH B 4 404 327 HOH HOH . R 7 HOH B 5 405 287 HOH HOH . R 7 HOH B 6 406 315 HOH HOH . R 7 HOH B 7 407 281 HOH HOH . R 7 HOH B 8 408 283 HOH HOH . R 7 HOH B 9 409 304 HOH HOH . R 7 HOH B 10 410 275 HOH HOH . R 7 HOH B 11 411 293 HOH HOH . R 7 HOH B 12 412 329 HOH HOH . R 7 HOH B 13 413 278 HOH HOH . R 7 HOH B 14 414 274 HOH HOH . R 7 HOH B 15 415 296 HOH HOH . R 7 HOH B 16 416 276 HOH HOH . R 7 HOH B 17 417 311 HOH HOH . R 7 HOH B 18 418 272 HOH HOH . R 7 HOH B 19 419 291 HOH HOH . R 7 HOH B 20 420 321 HOH HOH . R 7 HOH B 21 421 312 HOH HOH . R 7 HOH B 22 422 318 HOH HOH . R 7 HOH B 23 423 280 HOH HOH . R 7 HOH B 24 424 328 HOH HOH . R 7 HOH B 25 425 282 HOH HOH . R 7 HOH B 26 426 303 HOH HOH . R 7 HOH B 27 427 273 HOH HOH . R 7 HOH B 28 428 277 HOH HOH . R 7 HOH B 29 429 295 HOH HOH . R 7 HOH B 30 430 325 HOH HOH . R 7 HOH B 31 431 319 HOH HOH . R 7 HOH B 32 432 301 HOH HOH . R 7 HOH B 33 433 298 HOH HOH . R 7 HOH B 34 434 286 HOH HOH . R 7 HOH B 35 435 288 HOH HOH . R 7 HOH B 36 436 309 HOH HOH . R 7 HOH B 37 437 310 HOH HOH . R 7 HOH B 38 438 322 HOH HOH . R 7 HOH B 39 439 300 HOH HOH . R 7 HOH B 40 440 299 HOH HOH . R 7 HOH B 41 441 326 HOH HOH . R 7 HOH B 42 442 305 HOH HOH . R 7 HOH B 43 443 317 HOH HOH . R 7 HOH B 44 444 297 HOH HOH . R 7 HOH B 45 445 279 HOH HOH . R 7 HOH B 46 446 285 HOH HOH . R 7 HOH B 47 447 289 HOH HOH . R 7 HOH B 48 448 324 HOH HOH . R 7 HOH B 49 449 320 HOH HOH . R 7 HOH B 50 450 307 HOH HOH . R 7 HOH B 51 451 314 HOH HOH . R 7 HOH B 52 452 316 HOH HOH . R 7 HOH B 53 453 313 HOH HOH . S 7 HOH C 1 401 323 HOH HOH . S 7 HOH C 2 402 314 HOH HOH . S 7 HOH C 3 403 288 HOH HOH . S 7 HOH C 4 404 302 HOH HOH . S 7 HOH C 5 405 307 HOH HOH . S 7 HOH C 6 406 299 HOH HOH . S 7 HOH C 7 407 311 HOH HOH . S 7 HOH C 8 408 319 HOH HOH . S 7 HOH C 9 409 315 HOH HOH . S 7 HOH C 10 410 286 HOH HOH . S 7 HOH C 11 411 273 HOH HOH . S 7 HOH C 12 412 305 HOH HOH . S 7 HOH C 13 413 318 HOH HOH . S 7 HOH C 14 414 284 HOH HOH . S 7 HOH C 15 415 295 HOH HOH . S 7 HOH C 16 416 275 HOH HOH . S 7 HOH C 17 417 334 HOH HOH . S 7 HOH C 18 418 301 HOH HOH . S 7 HOH C 19 419 308 HOH HOH . S 7 HOH C 20 420 331 HOH HOH . S 7 HOH C 21 421 337 HOH HOH . S 7 HOH C 22 422 278 HOH HOH . S 7 HOH C 23 423 292 HOH HOH . S 7 HOH C 24 424 335 HOH HOH . S 7 HOH C 25 425 309 HOH HOH . S 7 HOH C 26 426 274 HOH HOH . S 7 HOH C 27 427 327 HOH HOH . S 7 HOH C 28 428 283 HOH HOH . S 7 HOH C 29 429 282 HOH HOH . S 7 HOH C 30 430 287 HOH HOH . S 7 HOH C 31 431 310 HOH HOH . S 7 HOH C 32 432 276 HOH HOH . S 7 HOH C 33 433 294 HOH HOH . S 7 HOH C 34 434 306 HOH HOH . S 7 HOH C 35 435 289 HOH HOH . S 7 HOH C 36 436 326 HOH HOH . S 7 HOH C 37 437 303 HOH HOH . S 7 HOH C 38 438 285 HOH HOH . S 7 HOH C 39 439 297 HOH HOH . S 7 HOH C 40 440 300 HOH HOH . S 7 HOH C 41 441 313 HOH HOH . S 7 HOH C 42 442 329 HOH HOH . S 7 HOH C 43 443 317 HOH HOH . S 7 HOH C 44 444 291 HOH HOH . S 7 HOH C 45 445 339 HOH HOH . S 7 HOH C 46 446 332 HOH HOH . S 7 HOH C 47 447 279 HOH HOH . S 7 HOH C 48 448 325 HOH HOH . S 7 HOH C 49 449 298 HOH HOH . S 7 HOH C 50 450 293 HOH HOH . S 7 HOH C 51 451 281 HOH HOH . S 7 HOH C 52 452 277 HOH HOH . S 7 HOH C 53 453 340 HOH HOH . S 7 HOH C 54 454 296 HOH HOH . S 7 HOH C 55 455 328 HOH HOH . S 7 HOH C 56 456 280 HOH HOH . S 7 HOH C 57 457 336 HOH HOH . S 7 HOH C 58 458 321 HOH HOH . S 7 HOH C 59 459 330 HOH HOH . S 7 HOH C 60 460 304 HOH HOH . S 7 HOH C 61 461 312 HOH HOH . S 7 HOH C 62 462 316 HOH HOH . S 7 HOH C 63 463 290 HOH HOH . S 7 HOH C 64 464 324 HOH HOH . S 7 HOH C 65 465 320 HOH HOH . S 7 HOH C 66 466 322 HOH HOH . S 7 HOH C 67 467 333 HOH HOH . S 7 HOH C 68 468 338 HOH HOH . T 7 HOH D 1 401 328 HOH HOH . T 7 HOH D 2 402 290 HOH HOH . T 7 HOH D 3 403 303 HOH HOH . T 7 HOH D 4 404 320 HOH HOH . T 7 HOH D 5 405 326 HOH HOH . T 7 HOH D 6 406 277 HOH HOH . T 7 HOH D 7 407 317 HOH HOH . T 7 HOH D 8 408 278 HOH HOH . T 7 HOH D 9 409 285 HOH HOH . T 7 HOH D 10 410 309 HOH HOH . T 7 HOH D 11 411 336 HOH HOH . T 7 HOH D 12 412 335 HOH HOH . T 7 HOH D 13 413 289 HOH HOH . T 7 HOH D 14 414 302 HOH HOH . T 7 HOH D 15 415 283 HOH HOH . T 7 HOH D 16 416 284 HOH HOH . T 7 HOH D 17 417 274 HOH HOH . T 7 HOH D 18 418 288 HOH HOH . T 7 HOH D 19 419 308 HOH HOH . T 7 HOH D 20 420 301 HOH HOH . T 7 HOH D 21 421 311 HOH HOH . T 7 HOH D 22 422 275 HOH HOH . T 7 HOH D 23 423 297 HOH HOH . T 7 HOH D 24 424 296 HOH HOH . T 7 HOH D 25 425 310 HOH HOH . T 7 HOH D 26 426 329 HOH HOH . T 7 HOH D 27 427 334 HOH HOH . T 7 HOH D 28 428 282 HOH HOH . T 7 HOH D 29 429 280 HOH HOH . T 7 HOH D 30 430 273 HOH HOH . T 7 HOH D 31 431 324 HOH HOH . T 7 HOH D 32 432 287 HOH HOH . T 7 HOH D 33 433 281 HOH HOH . T 7 HOH D 34 434 318 HOH HOH . T 7 HOH D 35 435 312 HOH HOH . T 7 HOH D 36 436 298 HOH HOH . T 7 HOH D 37 437 305 HOH HOH . T 7 HOH D 38 438 293 HOH HOH . T 7 HOH D 39 439 307 HOH HOH . T 7 HOH D 40 440 321 HOH HOH . T 7 HOH D 41 441 323 HOH HOH . T 7 HOH D 42 442 313 HOH HOH . T 7 HOH D 43 443 286 HOH HOH . T 7 HOH D 44 444 304 HOH HOH . T 7 HOH D 45 445 316 HOH HOH . T 7 HOH D 46 446 315 HOH HOH . T 7 HOH D 47 447 292 HOH HOH . T 7 HOH D 48 448 314 HOH HOH . T 7 HOH D 49 449 332 HOH HOH . T 7 HOH D 50 450 306 HOH HOH . T 7 HOH D 51 451 279 HOH HOH . T 7 HOH D 52 452 300 HOH HOH . T 7 HOH D 53 453 291 HOH HOH . T 7 HOH D 54 454 333 HOH HOH . T 7 HOH D 55 455 299 HOH HOH . T 7 HOH D 56 456 319 HOH HOH . T 7 HOH D 57 457 276 HOH HOH . T 7 HOH D 58 458 327 HOH HOH . T 7 HOH D 59 459 294 HOH HOH . T 7 HOH D 60 460 295 HOH HOH . T 7 HOH D 61 461 331 HOH HOH . T 7 HOH D 62 462 325 HOH HOH . T 7 HOH D 63 463 330 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 O O01 6YW . . . N 6 -11.882 52.666 -35.543 1 73.11 ? O01 6YW 301 D 1 HETATM 2 P P02 6YW . . . N 6 -12.565 53.232 -34.354 1 85.65 ? P02 6YW 301 D 1 HETATM 3 O O03 6YW . . . N 6 -12.453 52.212 -33.266 1 82.13 -1 O03 6YW 301 D 1 HETATM 4 O O04 6YW . . . N 6 -11.862 54.502 -33.812 1 87.14 ? O04 6YW 301 D 1 HETATM 5 P P05 6YW . . . N 6 -11.38 55.743 -34.617 1 78.36 ? P05 6YW 301 D 1 HETATM 6 O O06 6YW . . . N 6 -9.929 55.704 -34.993 1 72.12 -1 O06 6YW 301 D 1 HETATM 7 O O07 6YW . . . N 6 -11.45 56.962 -33.659 1 82.43 ? O07 6YW 301 D 1 HETATM 8 P P08 6YW . . . N 6 -12.744 57.752 -33.358 1 87.57 ? P08 6YW 301 D 1 HETATM 9 O O09 6YW . . . N 6 -13.916 56.81 -33.234 1 82.07 -1 O09 6YW 301 D 1 HETATM 10 O O10 6YW . . . N 6 -12.916 58.735 -34.559 1 84.47 ? O10 6YW 301 D 1 HETATM 11 P P11 6YW . . . N 6 -13.855 59.973 -34.689 1 78.14 ? P11 6YW 301 D 1 HETATM 12 O O12 6YW . . . N 6 -14.977 59.568 -35.588 1 67.54 -1 O12 6YW 301 D 1 HETATM 13 O O13 6YW . . . N 6 -13.053 61.175 -35.306 1 78.52 ? O13 6YW 301 D 1 HETATM 14 P P14 6YW . . . N 6 -11.811 61.275 -36.277 1 78.73 ? P14 6YW 301 D 1 HETATM 15 O O15 6YW . . . N 6 -10.739 61.834 -35.382 1 71.21 -1 O15 6YW 301 D 1 HETATM 16 O O16 6YW . . . N 6 -12.353 62.206 -37.416 1 58.59 ? O16 6YW 301 D 1 HETATM 17 P P17 6YW . . . N 6 -11.932 63.648 -37.81 1 50.09 ? P17 6YW 301 D 1 HETATM 18 O O18 6YW . . . N 6 -10.526 63.87 -37.496 1 50.88 -1 O18 6YW 301 D 1 HETATM 19 O O19 6YW . . . N 6 -12.727 64.685 -37.131 1 50.35 -1 O19 6YW 301 D 1 HETATM 20 O O20 6YW . . . N 6 -12.136 63.748 -39.263 1 50.23 ? O20 6YW 301 D 1 HETATM 21 O O21 6YW . . . N 6 -11.251 59.999 -36.849 1 58.22 ? O21 6YW 301 D 1 HETATM 22 O O22 6YW . . . N 6 -14.399 60.484 -33.39 1 76.9 ? O22 6YW 301 D 1 HETATM 23 O O23 6YW . . . N 6 -12.557 58.487 -32.084 1 76.49 ? O23 6YW 301 D 1 HETATM 24 O O24 6YW . . . N 6 -12.232 55.885 -35.842 1 73.17 ? O24 6YW 301 D 1 HETATM 25 O O25 6YW . . . N 6 -14.013 53.503 -34.671 1 79.6 -1 O25 6YW 301 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #