Structure of PDB 3vk7 Chain A Binding Site BS01

Receptor Information

>3vk7 Chain A (length=288) Species: 212035 (Acanthamoeba polyphaga mimivirus)

PQGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLK
VSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSLFEAKYTRAVLS
FDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIK
KYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIEN
LWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFL
VYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQKLE

Ligand information

>3vk7 Chain C (length=13)

gtagacgtggacg

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vk7 Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): Y95 M113 R114 N115 F116 S272 G273 K274 N275
• Binding residue (residue number reindexed from 1): Y94 M112 R113 N114 F115 S271 G272 K273 N274

Enzymatic activity

• Enzyme Commision number: 3.2.2.23: DNA-formamidopyrimidine glycosylase.
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

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

External links

• PDB: RCSB:3vk7, PDBe:3vk7, PDBj:3vk7
• PDBsum: 3vk7
• PubMed: 22170059
• UniProt: Q5UQ00|FPG_MIMIV Probable formamidopyrimidine-DNA glycosylase (Gene Name=MIMI_L315)