Structure of PDB 6ki3 Chain B

Receptor sequence

>6ki3B (length=300) Species: 561443 (African swine fever virus tick/South Africa/Pretoriuskop Pr4/1996)

SGGGMFGAFVSHRLWSDSGCTTTCITNSIANYVAFGEQIGFPFKSAQVFI
AGPRKAVINIQEDDKVELLKMIVKHNLWVVAHGTYLDVPWSRRSAFVTHF
IQQELLICKEVGIKGLVLHLGAVEPELIVEGLKKIKPVEGVVIYLETPHN
KHHTYKYSTMEQIKELFLRIRNTRLKQIGLCIDTAHIWSSGVNISSYNDA
GQWLRSLENIHSVIPPSHIMFHLNDAATECGSGIDRHASLFEGMIWKSYS
HKIKQSGLYCFVEYITRHQCPAILERNLGSSMQLQTALTAEFTTLKSLLK

3D structure

• PDB: 6ki3 A unique DNA-binding mode of African swine fever virus AP endonuclease.
• Chain: B
• 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	B	Y81 R232	Y85 R236
BS02	dna	B	F5 S7 H8 F45 G48 P49 R50 Y81 H115 E142 H182 H233 E271 N273	F9 S11 H12 F49 G52 P53 R54 Y85 H119 E146 H186 H237 E275 N277
BS03	dna	B	S14 R50 K51 Y81 L82 V84 S87 R89 F92	S18 R54 K55 Y85 L86 V88 S91 R93 F96
BS04	ZN	B	H182 D231 H233	H186 D235 H237
BS05	ZN	B	E142 D179 H218 E271	E146 D183 H222 E275
BS06	ZN	B	H78 H115 E142	H82 H119 E146

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)