Structure of PDB 8ka5 Chain A Binding Site BS04

Receptor Information
>8ka5 Chain A (length=297) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QSEPWTVLAHKKPQKDWKAYNPKTMRPPPLPEGTKCVKVMTWNVNGLRGL
LKFESFSALQLAQRENFDILCLQETKLQVKDVEEIKKTLIDGYDHSFWSC
SVSKLGYSGTAIISRIKPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTY
VPNSGDGLKRLSYRIEEWDRTLSNHIKELEKSKPVVLTGDLNCAHEEIDI
FNPAGNKRSAGFTIEERQSFGANLLDKGFVDTFRKQHPGVVGYTYWGYRH
GGRKTNKGWRLDYFLVSQSIAANVHDSYILPDINGSDHCPIGLILKL
Ligand information
Ligand ID3DR
InChIInChI=1S/C5H11O6P/c6-4-1-2-10-5(4)3-11-12(7,8)9/h4-6H,1-3H2,(H2,7,8,9)/t4-,5+/m0/s1
InChIKeyBVOBPNSQIRMLCA-CRCLSJGQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(OCC1OCCC1O)(O)O
OpenEye OEToolkits 1.5.0C1CO[C@@H]([C@H]1O)COP(=O)(O)O
CACTVS 3.341O[C@H]1CCO[C@@H]1CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C1COC(C1O)COP(=O)(O)O
CACTVS 3.341O[CH]1CCO[CH]1CO[P](O)(O)=O
FormulaC5 H11 O6 P
Name1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE;
ABASIC DIDEOXYRIBOSE
ChEMBL
DrugBank
ZINCZINC000005848245
PDB chain8ka5 Chain B Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ka5 Arabidopsis AP endonuclease APR complex with 20bp THF-containing DNA
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Y389 N392 D429 N431 Y484 W498 L500 H527
Binding residue
(residue number reindexed from 1)		Y150 N153 D190 N192 Y245 W259 L261 H288
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.11.2: exodeoxyribonuclease III.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003824 catalytic activity
GO:0004518 nuclease activity
GO:0004519 endonuclease activity
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8ka5, PDBe:8ka5, PDBj:8ka5
PDBsum8ka5
PubMed38503293
UniProtP45951|ARP_ARATH DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic (Gene Name=ARP)

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