3VM8 | pdb_00003vm8

Crystal structure of the human APOBEC3C having HIV-1 Vif-binding interface

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3vm8a_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3vm8b_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cytidine deaminase-like	8105529	3001838	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytidine deaminase-like	8105529	3001838	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	APOBEC_N	e3vm8A1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)
B	APOBEC_N	e3vm8B1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18782	Novel AID APOBEC clade 2 (NAD2)	Novel AID APOBEC clade 2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable DNA dC->dU-editing enzyme APOBEC-3C	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	DNA cytosine deamination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA deamination DNA modification macromolecule modification metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular process DNA cytosine deamination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA deamination DNA modification macromolecule modification metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process transposable element silencing regulation of macromolecule biosynthetic process regulation of metabolic process cytidine to uridine editing RNA metabolic process RNA modification base conversion or substitution editing negative regulation of viral genome replication viral life cycle negative regulation of viral process regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of RNA biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process viral RNA genome replication negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process single stranded viral RNA replication via double stranded DNA intermediate negative regulation of RNA metabolic process defense response to virus response to virus positive regulation of biological process positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression DNA-templated transcription initiation positive regulation of gene expression transcription initiation-coupled chromatin remodeling clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050610	APOBEC Cytidine Deaminase	Family
A, B	IPR016193	Cytidine deaminase-like	Homologous Superfamily
A, B	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, B	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9NRW3	acute myeloid leukemia Psychotic Disorders lung carcinoma subependymal giant cell astrocytoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.