Structure of PDB 8ka4 Chain B Binding Site BS01

Receptor Information
>8ka4 Chain B (length=296) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEPWTVLAHKKPQKDWKAYNPKTMRPPPLPEGTKCVKVMTWNVNGLRGLL
KFESFSALQLAQRENFDILCLQETKLQVKDVEEIKKTLIDGYDHSFWSCS
VSKLGYSGTAIISRIKPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYV
PNSGDGLKRLSYRIEEWDRTLSNHIKELEKSKPVVLTGDLNCAHEEIDIF
NPAGNKRSAGFTIEERQSFGANLLDKGFVDTFRKQHPGVVGYTYWGYRHG
GRKTNKGWRLDYFLVSQSIAANVHDSYILPDINGSDHCPIGLILKL
Ligand information
Ligand IDDG
InChIInChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyLTFMZDNNPPEQNG-KVQBGUIXSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3)COP(=O)(O)O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O7 P
Name2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL477487
DrugBankDB04457
ZINCZINC000001730395
PDB chain8ka4 Chain B Residue 601 [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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PDB8ka4 Arabidopsis AP endonuclease APR complex with 21bp THF-containing DNA
Resolution2.3 Å
Binding residue
(original residue number in PDB)		V318 C339 V341 H369
Binding residue
(residue number reindexed from 1)		V78 C99 V101 H129
Annotation score4
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:8ka4, PDBe:8ka4, PDBj:8ka4
PDBsum8ka4
PubMed38503293
UniProtP45951|ARP_ARATH DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic (Gene Name=ARP)

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