data_6Z81 # _model_server_result.job_id 7KxzIKlcFfnNutkVNQSREA _model_server_result.datetime_utc '2024-10-20 00:32:52' _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 6z81 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":404}' # _entry.id 6Z81 # _exptl.entry_id 6Z81 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 490.362 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 109.38 _cell.angle_beta 92 _cell.angle_gamma 116.94 _cell.entry_id 6Z81 _cell.length_a 63.23 _cell.length_b 69.25 _cell.length_c 86.54 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Z81 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,I,J,K,L,M,N,O,P,Y,Z,AA,BA,CA,HA,JA 1 1 B,D,Q,R,S,T,U,V,W,X,DA,EA,FA,GA,IA,KA 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 T N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 111 A HIS 111 1_555 G ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc2 A NE2 HIS 115 A HIS 115 1_555 G ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc3 A OD1 ASP 300 A ASP 300 1_555 G ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc4 G ZN ZN . A ZN 403 1_555 H OX QCB . A QCB 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc5 G ZN ZN . A ZN 403 1_555 H OP1 QCB . A QCB 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc6 N O1 PEG . A PEG 410 1_555 Y NA NA . C NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc7 B NE2 HIS 111 B HIS 111 1_555 S ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc8 B NE2 HIS 115 B HIS 115 1_555 S ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc9 B OD1 ASP 300 B ASP 300 1_555 S ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc10 S ZN ZN . B ZN 403 1_555 T OP3 QCB . B QCB 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc11 S ZN ZN . B ZN 403 1_555 T OX QCB . B QCB 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? # _chem_comp.formula 'C16 H23 N6 O10 P' _chem_comp.formula_weight 490.362 _chem_comp.id QCB _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{S},3~{R})-2-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]ethanoylamino]-3-oxidanyl-butanoic acid' _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 CGX CBX QCB sing 338 n n CBX OGX QCB sing 339 n n CBX CAX QCB sing 340 n n NX CAX QCB sing 341 n n NX CCA QCB sing 342 n n CAX CX QCB sing 343 n n CCA CP2 QCB sing 344 n n CCA OCA QCB doub 345 n n CP2 P1 QCB sing 346 n n CX OX QCB doub 347 n n CX OXT QCB sing 348 n n OP3 P1 QCB doub 349 n n P1 OP1 QCB sing 350 n n P1 O5' QCB sing 351 n n C5' O5' QCB sing 352 n n C5' C4' QCB sing 353 n n C3' C4' QCB sing 354 n n C3' O3' QCB sing 355 n n C3' C2' QCB sing 356 n n C4' O4' QCB sing 357 n n C2' O2' QCB sing 358 n n C2' C1' QCB sing 359 n n O4' C1' QCB sing 360 n n C1' N9 QCB sing 361 n n C8 N9 QCB sing 362 n y C8 N7 QCB doub 363 n y N9 C4 QCB sing 364 n y N7 C5 QCB sing 365 n y C4 C5 QCB doub 366 n y C4 N3 QCB sing 367 n y C5 C6 QCB sing 368 n y N3 C2 QCB doub 369 n y C6 N6 QCB sing 370 n n C6 N1 QCB doub 371 n y C2 N1 QCB sing 372 n y C2 H1 QCB sing 373 n n CAX H2 QCB sing 374 n n CBX H3 QCB sing 375 n n CGX H4 QCB sing 376 n n CGX H5 QCB sing 377 n n CGX H6 QCB sing 378 n n OGX H7 QCB sing 379 n n NX H8 QCB sing 380 n n CP2 H9 QCB sing 381 n n CP2 H10 QCB sing 382 n n OP1 H11 QCB sing 383 n n C5' H12 QCB sing 384 n n C5' H13 QCB sing 385 n n C4' H14 QCB sing 386 n n C3' H15 QCB sing 387 n n O3' H16 QCB sing 388 n n C2' H17 QCB sing 389 n n O2' H18 QCB sing 390 n n C1' H19 QCB sing 391 n n C8 H20 QCB sing 392 n n N6 H21 QCB sing 393 n n N6 H22 QCB sing 394 n n OXT H23 QCB sing 395 n n # _atom_sites.entry_id 6Z81 _atom_sites.fract_transf_matrix[1][1] 0.015815 _atom_sites.fract_transf_matrix[1][2] 0.008037 _atom_sites.fract_transf_matrix[1][3] 0.004006 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016198 _atom_sites.fract_transf_matrix[2][3] 0.006865 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012558 _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 3 NI A 1 401 353 NI NI . F 3 NI A 1 402 355 NI NI . G 4 ZN A 1 403 360 ZN ZN . H 5 QCB A 1 404 361 QCB BK9 . I 6 SO4 A 1 405 387 SO4 SO4 . J 6 SO4 A 1 406 388 SO4 SO4 . K 7 NA A 1 407 394 NA NA . L 8 ACT A 1 408 401 ACT ACT . M 8 ACT A 1 409 402 ACT ACT . N 9 PEG A 1 410 403 PEG PEG . O 9 PEG A 1 411 501 PEG PEG . P 8 ACT A 1 412 601 ACT ACT . Q 3 NI B 1 401 353 NI NI . R 3 NI B 1 402 354 NI NI . S 4 ZN B 1 403 360 ZN ZN . T 5 QCB B 1 404 361 QCB BK9 . U 6 SO4 B 1 405 387 SO4 SO4 . V 6 SO4 B 1 406 388 SO4 SO4 . W 8 ACT B 1 407 401 ACT ACT . X 9 PEG B 1 408 501 PEG PEG . Y 7 NA C 1 301 391 NA NA . Z 10 AMP C 1 302 401 AMP AMP . AA 8 ACT C 1 303 402 ACT ACT . BA 8 ACT C 1 304 403 ACT ACT . CA 8 ACT C 1 305 404 ACT ACT . DA 7 NA D 1 301 395 NA NA . EA 10 AMP D 1 302 401 AMP AMP . FA 8 ACT D 1 303 402 ACT ACT . GA 8 ACT D 1 304 501 ACT ACT . HA 11 HOH A 1 501 36 HOH HOH . HA 11 HOH A 2 502 418 HOH HOH . HA 11 HOH A 3 503 431 HOH HOH . HA 11 HOH A 4 504 416 HOH HOH . HA 11 HOH A 5 505 412 HOH HOH . HA 11 HOH A 6 506 37 HOH HOH . HA 11 HOH A 7 507 433 HOH HOH . HA 11 HOH A 8 508 35 HOH HOH . HA 11 HOH A 9 509 421 HOH HOH . HA 11 HOH A 10 510 420 HOH HOH . HA 11 HOH A 11 511 33 HOH HOH . HA 11 HOH A 12 512 414 HOH HOH . HA 11 HOH A 13 513 426 HOH HOH . HA 11 HOH A 14 514 425 HOH HOH . HA 11 HOH A 15 515 422 HOH HOH . HA 11 HOH A 16 516 410 HOH HOH . HA 11 HOH A 17 517 421 HOH HOH . HA 11 HOH A 18 518 430 HOH HOH . HA 11 HOH A 19 519 407 HOH HOH . HA 11 HOH A 20 520 429 HOH HOH . HA 11 HOH A 21 521 14 HOH HOH . HA 11 HOH A 22 522 26 HOH HOH . HA 11 HOH A 23 523 27 HOH HOH . HA 11 HOH A 24 524 9 HOH HOH . HA 11 HOH A 25 525 7 HOH HOH . HA 11 HOH A 26 526 440 HOH HOH . HA 11 HOH A 27 527 16 HOH HOH . HA 11 HOH A 28 528 6 HOH HOH . HA 11 HOH A 29 529 11 HOH HOH . HA 11 HOH A 30 530 17 HOH HOH . IA 11 HOH B 1 501 421 HOH HOH . IA 11 HOH B 2 502 423 HOH HOH . IA 11 HOH B 3 503 426 HOH HOH . IA 11 HOH B 4 504 434 HOH HOH . IA 11 HOH B 5 505 411 HOH HOH . IA 11 HOH B 6 506 427 HOH HOH . IA 11 HOH B 7 507 31 HOH HOH . IA 11 HOH B 8 508 410 HOH HOH . IA 11 HOH B 9 509 406 HOH HOH . IA 11 HOH B 10 510 417 HOH HOH . IA 11 HOH B 11 511 430 HOH HOH . IA 11 HOH B 12 512 433 HOH HOH . IA 11 HOH B 13 513 414 HOH HOH . IA 11 HOH B 14 514 436 HOH HOH . IA 11 HOH B 15 515 424 HOH HOH . IA 11 HOH B 16 516 410 HOH HOH . IA 11 HOH B 17 517 412 HOH HOH . IA 11 HOH B 18 518 432 HOH HOH . IA 11 HOH B 19 519 5 HOH HOH . IA 11 HOH B 20 520 428 HOH HOH . IA 11 HOH B 21 521 439 HOH HOH . IA 11 HOH B 22 522 12 HOH HOH . IA 11 HOH B 23 523 13 HOH HOH . IA 11 HOH B 24 524 34 HOH HOH . IA 11 HOH B 25 525 418 HOH HOH . IA 11 HOH B 26 526 10 HOH HOH . IA 11 HOH B 27 527 1 HOH HOH . IA 11 HOH B 28 528 18 HOH HOH . IA 11 HOH B 29 529 23 HOH HOH . IA 11 HOH B 30 530 3 HOH HOH . IA 11 HOH B 31 531 29 HOH HOH . IA 11 HOH B 32 532 4 HOH HOH . JA 11 HOH C 1 401 406 HOH HOH . JA 11 HOH C 2 402 422 HOH HOH . JA 11 HOH C 3 403 419 HOH HOH . JA 11 HOH C 4 404 414 HOH HOH . JA 11 HOH C 5 405 427 HOH HOH . JA 11 HOH C 6 406 409 HOH HOH . JA 11 HOH C 7 407 421 HOH HOH . JA 11 HOH C 8 408 28 HOH HOH . JA 11 HOH C 9 409 429 HOH HOH . JA 11 HOH C 10 410 428 HOH HOH . JA 11 HOH C 11 411 32 HOH HOH . JA 11 HOH C 12 412 425 HOH HOH . JA 11 HOH C 13 413 417 HOH HOH . JA 11 HOH C 14 414 424 HOH HOH . JA 11 HOH C 15 415 418 HOH HOH . JA 11 HOH C 16 416 24 HOH HOH . JA 11 HOH C 17 417 15 HOH HOH . JA 11 HOH C 18 418 21 HOH HOH . KA 11 HOH D 1 401 413 HOH HOH . KA 11 HOH D 2 402 409 HOH HOH . KA 11 HOH D 3 403 419 HOH HOH . KA 11 HOH D 4 404 423 HOH HOH . KA 11 HOH D 5 405 30 HOH HOH . KA 11 HOH D 6 406 425 HOH HOH . KA 11 HOH D 7 407 411 HOH HOH . KA 11 HOH D 8 408 412 HOH HOH . KA 11 HOH D 9 409 414 HOH HOH . KA 11 HOH D 10 410 419 HOH HOH . KA 11 HOH D 11 411 415 HOH HOH . KA 11 HOH D 12 412 416 HOH HOH . KA 11 HOH D 13 413 407 HOH HOH . KA 11 HOH D 14 414 417 HOH HOH . KA 11 HOH D 15 415 427 HOH HOH . KA 11 HOH D 16 416 8 HOH HOH . KA 11 HOH D 17 417 426 HOH HOH . KA 11 HOH D 18 418 22 HOH HOH . KA 11 HOH D 19 419 25 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 N N1 QCB . . . H 5 40.668 -18.089 -15.297 1 36.38 ? N1 QCB 404 A 1 HETATM 2 C C2 QCB . . . H 5 39.369 -17.932 -15.611 1 32.84 ? C2 QCB 404 A 1 HETATM 3 N N3 QCB . . . H 5 38.794 -18.173 -16.793 1 32.26 ? N3 QCB 404 A 1 HETATM 4 C C4 QCB . . . H 5 39.687 -18.589 -17.717 1 32.73 ? C4 QCB 404 A 1 HETATM 5 C C5 QCB . . . H 5 41.06 -18.806 -17.495 1 29.39 ? C5 QCB 404 A 1 HETATM 6 C C6 QCB . . . H 5 41.506 -18.523 -16.228 1 32.01 ? C6 QCB 404 A 1 HETATM 7 C CX QCB . . . H 5 33.492 -24.758 -25.096 1 43.12 ? CX QCB 404 A 1 HETATM 8 O OX QCB . . . H 5 34.382 -25.525 -24.658 1 42.66 ? OX QCB 404 A 1 HETATM 9 C CAX QCB . . . H 5 33.71 -23.887 -26.337 1 39.08 ? CAX QCB 404 A 1 HETATM 10 C CBX QCB . . . H 5 33.114 -24.498 -27.612 1 36.19 ? CBX QCB 404 A 1 HETATM 11 C CGX QCB . . . H 5 33.914 -24.113 -28.843 1 28.38 ? CGX QCB 404 A 1 HETATM 12 O OGX QCB . . . H 5 32.845 -25.873 -27.574 1 39.26 ? OGX QCB 404 A 1 HETATM 13 N NX QCB . . . H 5 35.115 -23.552 -26.437 1 36.72 ? NX QCB 404 A 1 HETATM 14 C CCA QCB . . . H 5 35.557 -22.491 -25.549 1 33.81 ? CCA QCB 404 A 1 HETATM 15 C CP2 QCB . . . H 5 36.992 -22.046 -25.512 1 31.3 ? CP2 QCB 404 A 1 HETATM 16 O OCA QCB . . . H 5 34.799 -21.946 -24.827 1 36.94 ? OCA QCB 404 A 1 HETATM 17 P P1 QCB . . . H 5 37.773 -22.686 -23.941 1 30.83 ? P1 QCB 404 A 1 HETATM 18 O OP3 QCB . . . H 5 39.239 -22.648 -24.233 1 32.8 ? OP3 QCB 404 A 1 HETATM 19 O OP1 QCB . . . H 5 37.344 -24.076 -23.582 1 32.19 ? OP1 QCB 404 A 1 HETATM 20 O O5' QCB . . . H 5 37.427 -21.759 -22.642 1 31.04 ? O5' QCB 404 A 1 HETATM 21 C C5' QCB . . . H 5 37.686 -20.392 -22.725 1 32.39 ? C5' QCB 404 A 1 HETATM 22 C C4' QCB . . . H 5 37.166 -19.758 -21.492 1 32.93 ? C4' QCB 404 A 1 HETATM 23 C C3' QCB . . . H 5 37.191 -18.28 -21.64 1 38.13 ? C3' QCB 404 A 1 HETATM 24 O O3' QCB . . . H 5 35.845 -17.799 -21.397 1 38.34 ? O3' QCB 404 A 1 HETATM 25 C C2' QCB . . . H 5 38.166 -17.787 -20.641 1 40.93 ? C2' QCB 404 A 1 HETATM 26 O O2' QCB . . . H 5 37.755 -16.536 -20.059 1 44.12 ? O2' QCB 404 A 1 HETATM 27 C C1' QCB . . . H 5 38.274 -18.869 -19.613 1 36.31 ? C1' QCB 404 A 1 HETATM 28 O O4' QCB . . . H 5 38.032 -20.117 -20.362 1 33.42 ? O4' QCB 404 A 1 HETATM 29 N N9 QCB . . . H 5 39.545 -18.899 -18.948 1 33.56 ? N9 QCB 404 A 1 HETATM 30 C C8 QCB . . . H 5 40.61 -19.303 -19.499 1 28.79 ? C8 QCB 404 A 1 HETATM 31 N N7 QCB . . . H 5 41.638 -19.324 -18.654 1 27.09 ? N7 QCB 404 A 1 HETATM 32 N N6 QCB . . . H 5 42.903 -18.698 -15.89 1 29.71 ? N6 QCB 404 A 1 HETATM 33 O OXT QCB . . . H 5 32.426 -24.648 -24.455 1 46.46 ? OXT QCB 404 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 33 #