Structure of PDB 6khy Chain C

Receptor sequence

>6khyC (length=299) Species: 561443 (African swine fever virus tick/South Africa/Pretoriuskop Pr4/1996)

GGGMFGAFVSHRLWSDSGCTTTCITNSIANYVAFGEQIGFPFKSAQVFIA
GPRKAVINIQEDDKVELLKMIVKHNLWVVAHGTYLDVPWSRRSAFVTHFI
QQELLICKEVGIKGLVLHLGAVEPELIVEGLKKIKPVEGVVIYLETPHNK
HHTYKYSTMEQIKELFLRIRNTRLKQIGLCIDTAHIWSSGVNISSYNDAG
QWLRSLENIHSVIPPSHIMFHLNDAATECGSGIDRHASLFEGMIWKSYSH
KIKQSGLYCFVEYITRHQCPAILERNLGSSMQLQTALTAEFTTLKSLLK

3D structure

• PDB: 6khy A unique DNA-binding mode of African swine fever virus AP endonuclease.
• Chain: C
• Resolution: 3.008 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	C	Y81 D231 R232 H233	Y84 D234 R235 H236
BS02	dna	C	Y81 L82 V84 A118 N146 K147 H148 H149	Y84 L85 V87 A121 N149 K150 H151 H152
BS03	ZN	C	H182 D231 H233	H185 D234 H236
BS04	ZN	C	E142 D179 H218 E271	E145 D182 H221 E274
BS05	ZN	C	H78 H115 E142	H81 H118 E145

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004519 endonuclease activity
• GO:0004527 exonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

Cellular Component

• GO:0030430 host cell cytoplasm
• GO:0042025 host cell nucleus
• GO:0044423 virion component

External links

• PDB: RCSB:6khy, PDBe:6khy, PDBj:6khy
• PDBsum: 6khy
• PubMed: 32194979
• UniProt: P0C9C6|APE_ASFP4 Probable AP endonuclease (Gene Name=Pret-146)