Structure of PDB 8fim Chain B

Receptor sequence
>8fimB (length=187) Species: 9606 (Homo sapiens) [Search protein sequence]
RHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDNGTSVKMDQHRGFLHNQA
KNLLCGFYGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGE
VRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFK
HCWDTFVDHQGCPFQPWDGLDEHSQALSGRLRAILQN
3D structure
PDB8fim DNA-based inhibitors restrict mutagenic activity of APOBEC3 in cells
ChainB
Resolution2.22 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number 3.5.4.38: single-stranded DNA cytosine deaminase.
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 R28 H29 T31 N57 A59 K60 H70 W98 S99 Y130 D131 Y132 R19 H20 T22 N48 A50 K51 H61 W89 S90 Y121 D122 Y123
BS02 IHP B K159 H160 D163 K150 H151 D154
BS03 ZN B H70 C101 C106 H61 C92 C97
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8fim, PDBe:8fim, PDBj:8fim
PDBsum8fim
PubMed37821454
UniProtP31941|ABC3A_HUMAN DNA dC->dU-editing enzyme APOBEC-3A (Gene Name=APOBEC3A)

[Back to BioLiP]