Structure of PDB 3vk7 Chain A

Receptor sequence
>3vk7A (length=288) Species: 212035 (Acanthamoeba polyphaga mimivirus) [Search protein sequence]
PQGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLK
VSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSLFEAKYTRAVLS
FDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIK
KYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIEN
LWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFL
VYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQKLE
3D structure
PDB3vk7 Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA
ChainA
Resolution2.1 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.2.2.23: DNA-formamidopyrimidine glycosylase.
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
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 Y95 M113 R114 N115 F116 S272 G273 K274 N275 Y94 M112 R113 N114 F115 S271 G272 K273 N274
BS02 dna A K60 G83 L84 R114 F116 G172 N173 Y174 Y221 Y253 R254 N275 R277 T278 Y280 K59 G82 L83 R113 F115 G171 N172 Y173 Y220 Y252 R253 N274 R276 T277 Y279
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0008270 zinc ion binding
GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0016829 lyase activity
GO:0019104 DNA N-glycosylase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0006281 DNA repair
GO:0006284 base-excision repair

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vk7, PDBe:3vk7, PDBj:3vk7
PDBsum3vk7
PubMed22170059
UniProtQ5UQ00|FPG_MIMIV Probable formamidopyrimidine-DNA glycosylase (Gene Name=MIMI_L315)

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