Structure of PDB 7d3v Chain B Binding Site BS01

Receptor Information

>7d3v Chain B (length=199) Species: 9606 (Homo sapiens)

MEASPASGPRHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDNGTSVKMDQ
HRGFLHNQAKNLNSGFYGRHAQLRFLDLVPSLQLDPAQIYRVTWFISWSP
CFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQV
SIMTYDEFKHCWDTFVDHQGQPFQPWDGLDEHSQALSGRLRAILQNQGN

Ligand information

>7d3v Chain C (length=10)

attttcaatt

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7d3v Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3
• Resolution: N/A
• Binding residue (original residue number in PDB): S219 N222 N223 G224 I225 R227 K229 K259 N260 N262 E380 H381 Q383 A384 R388
• Binding residue (residue number reindexed from 1): S20 N23 N24 G25 I26 R28 K30 K60 N61 N63 E181 H182 Q184 A185 R189

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:7d3v, PDBe:7d3v, PDBj:7d3v
• PDBsum: 7d3v
• UniProt: P31941|ABC3A_HUMAN DNA dC->dU-editing enzyme APOBEC-3A (Gene Name=APOBEC3A)