5W3V | pdb_00005w3v

Crystal Structure of macaque APOBEC3H in complex with RNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	APOBEC domain-like	8079976	4005403	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Cytidine deaminase-like	8087261	3001838	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Cytidine deaminase-like	8087261	3001838	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytidine deaminase-like	8087261	3001838	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytidine deaminase-like	8087261	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)
D	APOBEC_N	e5w3vD1	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)
C	APOBEC_N	e5w3vC1	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	e5w3vB1	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)
A	APOBEC_N	e5w3vA1	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
B, C, D	PF18771	APOBEC3 (APOBEC3)	APOBEC3	-	Family
A	PF18771	APOBEC3 (APOBEC3)	APOBEC3	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, G	RNA (5'-R(PAPAPCPCPCPCPGPGPGPC)-3')	-	-	-
E, H	RNA (5'-R(PAPAPCPCPCPGPGPGPGPA)-3')	-	-	-
B, C, D	Apobec3H	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 cytidine to uridine editing RNA metabolic process RNA modification 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 cytidine to uridine editing RNA metabolic process RNA modification base conversion or substitution editing 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 regulation of cellular process negative regulation of biological process viral life cycle 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 negative regulation of viral process viral RNA genome replication viral process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of viral genome replication negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process single stranded viral RNA replication via double stranded DNA intermediate macromolecule biosynthetic process regulation of viral process regulation of viral life cycle viral genome replication biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of viral genome replication regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of RNA metabolic process defense response to virus response to virus	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
A	Apobec3H	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 cytidine to uridine editing RNA metabolic process RNA modification 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 cytidine to uridine editing RNA metabolic process RNA modification base conversion or substitution editing 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 regulation of cellular process negative regulation of biological process viral life cycle 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 negative regulation of viral process viral RNA genome replication viral process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of viral genome replication negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process single stranded viral RNA replication via double stranded DNA intermediate macromolecule biosynthetic process regulation of viral process regulation of viral life cycle viral genome replication biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of viral genome replication regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of RNA metabolic process defense response to virus response to virus	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
B, C, D	IPR041512	APOBEC3H	Family
B, C, D	IPR050610	APOBEC Cytidine Deaminase	Family
B, C, D	IPR016193	Cytidine deaminase-like	Homologous Superfamily
B, C, D	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
B, C, D	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site
A	IPR041512	APOBEC3H	Family
A	IPR050610	APOBEC Cytidine Deaminase	Family
A	IPR016193	Cytidine deaminase-like	Homologous Superfamily
A	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, C, D	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

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.