Structure of PDB 8fim Chain B Binding Site BS01

Receptor Information

>8fim Chain B (length=187) Species: 9606 (Homo sapiens)

RHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDNGTSVKMDQHRGFLHNQA
KNLLCGFYGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGE
VRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFK
HCWDTFVDHQGCPFQPWDGLDEHSQALSGRLRAILQN

Ligand information

>8fim Chain H (length=13)

tgcgcttcgcgct

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fim DNA-based inhibitors restrict mutagenic activity of APOBEC3 in cells
• Resolution: 2.22 Å
• Binding residue (original residue number in PDB): R28 H29 T31 N57 A59 K60 H70 W98 S99 Y130 D131 Y132
• Binding residue (residue number reindexed from 1): R19 H20 T22 N48 A50 K51 H61 W89 S90 Y121 D122 Y123

Enzymatic activity

• Enzyme Commision number: 3.5.4.38: single-stranded DNA cytosine deaminase.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003824 catalytic activity
• GO:0004126 cytidine deaminase activity
• GO:0005515 protein binding
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0010526 retrotransposon silencing
• GO:0016554 cytidine to uridine editing
• GO:0044029 positive regulation of gene expression via chromosomal CpG island demethylation
• GO:0044355 clearance of foreign intracellular DNA
• GO:0045071 negative regulation of viral genome replication
• GO:0045087 innate immune response
• GO:0045869 negative regulation of single stranded viral RNA replication via double stranded DNA intermediate
• GO:0051607 defense response to virus
• GO:0070383 DNA cytosine deamination

Cellular Component

• GO:0000932 P-body
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm

External links

• PDB: RCSB:8fim, PDBe:8fim, PDBj:8fim
• PDBsum: 8fim
• PubMed: 37821454
• UniProt: P31941|ABC3A_HUMAN DNA dC->dU-editing enzyme APOBEC-3A (Gene Name=APOBEC3A)