Structure of PDB 8ka3 Chain A Binding Site BS04

Receptor Information
>8ka3 Chain A (length=291) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEPWTVLAHKKPQKDWKAYNPKTMRPPPLPEGTKCVKVMTWNVNGLRGLL
KFESFSALQLAQRENFDILCLQETKLQVKDVEEIKKTLIDGYDHSFWSCS
VSKLGYSGTAIISRIKPLSVRYGTGTEGRIVTAEFDSFYLINTYVPNSGD
GLKRLSYRIEEWDRTLSNHIKELEKSKPVVLTGDLNCAHEEIDIFNPAGN
KRSAGFTIEERQSFGANLLDKGFVDTFRKQHPGVVGYTYWGYRHGGRKTN
KGWRLDYFLVSQSIAANVHDSYILPDINGSDHCPIGLILKL
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 chain8ka3 Chain D 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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PDB8ka3 Arabidopsis AP endonuclease APR complex with 22bp THF-containing DNA
Resolution3.0 Å
Binding residue
(original residue number in PDB)		E313 Y389 N392 D429 N431 A449 Y484 W498 H527
Binding residue
(residue number reindexed from 1)		E73 Y144 N147 D184 N186 A204 Y239 W253 H282
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
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Biological Process
External links
PDB RCSB:8ka3, PDBe:8ka3, PDBj:8ka3
PDBsum8ka3
PubMed38503293
UniProtP45951|ARP_ARATH DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic (Gene Name=ARP)

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