Structure of PDB 6ki3 Chain A

Receptor sequence

>6ki3A (length=298) Species: 561443 (African swine fever virus tick/South Africa/Pretoriuskop Pr4/1996)

GGMFGAFVSHRLWSDSGCTTTCITNSIANYVAFGEQIGFPFKSAQVFIAG
PRKAVINIQEDDKVELLKMIVKHNLWVVAHGTYLDVPWSRRSAFVTHFIQ
QELLICKEVGIKGLVLHLGAVEPELIVEGLKKIKPVEGVVIYLETPHNKH
HTYKYSTMEQIKELFLRIRNTRLKQIGLCIDTAHIWSSGVNISSYNDAGQ
WLRSLENIHSVIPPSHIMFHLNDAATECGSGIDRHASLFEGMIWKSYSHK
IKQSGLYCFVEYITRHQCPAILERNLGSSMQLQTALTAEFTTLKSLLK

3D structure

• PDB: 6ki3 A unique DNA-binding mode of African swine fever virus AP endonuclease.
• Chain: A
• Resolution: 2.354 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	A	R50 Y81 D231 R232	R52 Y83 D233 R234
BS02	dna	A	F5 H8 F45 G48 P49 N55 Y81 H115 H182 H233 E271 N273	F7 H10 F47 G50 P51 N57 Y83 H117 H184 H235 E273 N275
BS03	dna	A	S14 R50 Y81 L82 V84 N146 K147 H148 H149	S16 R52 Y83 L84 V86 N148 K149 H150 H151
BS04	ZN	A	H182 D231 H233	H184 D233 H235
BS05	ZN	A	E142 D179 H218 E271	E144 D181 H220 E273
BS06	ZN	A	H78 H115 E142	H80 H117 E144

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:6ki3, PDBe:6ki3, PDBj:6ki3
• PDBsum: 6ki3
• PubMed: 32194979
• UniProt: P0C9C6|APE_ASFP4 Probable AP endonuclease (Gene Name=Pret-146)