Structure of PDB 8fth Chain A Binding Site BS01

Receptor Information

>8fth Chain A (length=1263) Species: 759272 (Thermochaetoides thermophila DSM 1495)

RLADQIVSLSFNRLQTLPPGQKILRFWSGFLFILHALSEKQIINSLRASI
YFLALEHLGTNSDEALAMVLRALQELMEKSSKAFWQALEQVPPNQLVEEI
FKSAAFRPLLNKSQVPALAAWMRALVRSLPSTSWSDLCETSLRHLFETFR
QSGRATCTLAGLVTLQQCLDGFLQQDSIDTGTGLIMVNQLLNRVVNYSEI
IIRAASLKPGDIYNVGISKAAMAIIHSALALDAKATEVEWAALIAEKPVQ
DRDSGALWETFLEMLWAGQLGHFELAKAMLMATLRLRSIEQFIPKRKEQL
KRELDKFNKRYQQQTTAIGKMLNRLTDFEPEVLDKLCSDQTIHPIVSSLI
HGEDAIREAGFQLLKAITSESQPSDAVGRMLEVYFTPFLNAFSQAVDKLT
ATKDANSPWSHMIPILKCSDFVLTGLCDPSSGQLRRKVLTTEEHAAVKRW
WECVWQAVDHSFRMMRIWHIKIDKKVMEDFCRDVMELGNKLLAQDGVMAS
SLAEDAISKAMREVLDPPRKCSYSLADMLQLRDKYLVMGIIETIKKLLSR
LQENEMNLPQRTRGHLDSMLKKTMDYLTKTNLTDVQRIELLKALGRLIPP
MDVLHQAILEWDIFHEGNDPPNGYRCGNVSDTYPDPYSYKQTFFPLLINE
AWRSFVTAKDETTSKPFGIKVLSRMTVDKFMEVTAAVPAQISKDRGLTEG
DIVIISKGEDPLNQPQELHCLSRIWKTTYKKDTVEVVYRLNAKGNQILPA
LTPGSEFQVVKITNMTTIEREYAALESLQYYDLMDEILKAQPSPMLTFGD
EAIKAVMDNYQLNPGQARAILNAKENDGFTLIQGPPGTGKTKTIVAMVGC
LLTKLLVCAPSNAAVDELVLRLKAGVKTMNGTFHKIEVLRLGRNAAVKDV
TLDELVKARMDRDQLHKEAGEIKAKLAEIRPQLDAMKLQREFDELKRRQA
HIGAKIDADKASGNTYARETEIKRRQIQQEILDKAQVLCATLSGSGHEMF
KNLNVEFETVIIDEAAQCVELSALIPLKYGCNKCILVGDPKQLPPTVLSY
GYDQSLFVRMQKNHPKDVHLLDMQYRMHPEISRFPSKEFYEGLLQDGADM
ARLRLQPWHQSVLLGPYRFFDVSLVNEEEVKVAMQLYMRFRSDTGKIGII
TPYKAQLQRLRQKFVERYGESITEQIEFNTTDAFQGRECEIIIFSCVRAS
PTGGIGFMTDIRRMNVGLTRARSSLWILGDSRALVQGEFWAKLIEDAKQR
DRYTNGNIMALLS

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 8fth Chain A Residue 2101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fth Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.
• Resolution: 3.17 Å
• Binding residue (original residue number in PDB): N1319 Q1322 P1342 T1344 G1345 K1346 T1347 R1405 Y1639
• Binding residue (residue number reindexed from 1): N813 Q816 P836 T838 G839 K840 T841 R871 Y1075
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.4.12: DNA helicase.

Gene Ontology

Molecular Function

• GO:0004386 helicase activity

External links

• PDB: RCSB:8fth, PDBe:8fth, PDBj:8fth
• PDBsum: 8fth
• PubMed: 37832548
• UniProt: G0S163