2NYT | pdb_00002nyt

The APOBEC2 Crystal Structure and Functional Implications for AID

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d2nytd1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains	APOBEC2 (APO2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2nytd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2nytc1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains	APOBEC2 (APO2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2nytc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2nytb1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains	APOBEC2 (APO2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2nytb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2nyta1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains	APOBEC2 (APO2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2nyta2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
D	SCOP2B Superfamily	Cytidine deaminase-like	8105520	3001838	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytidine deaminase-like	8105520	3001838	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytidine deaminase-like	8105520	3001838	SCOP2B (2022-06-29)
A	SCOP2 Family	APOBEC domain-like	8046990	4005403	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytidine deaminase-like	8105520	3001838	SCOP2 (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	e2nytD1	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	e2nytC1	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	e2nytB1	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	e2nytA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
C	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
B	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
A	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05240	APOBEC-like C-terminal domain (APOBEC_C)	APOBEC-like C-terminal domain	This domain is found at the C-termini of the Apolipoprotein B mRNA editing enzyme.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Probable C->U-editing enzyme APOBEC-2	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 RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding identical protein 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 RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding	mRNA modification RNA metabolic process primary metabolic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA modification macromolecule modification metabolic process cellular process macromolecule metabolic process cytidine to uridine editing base conversion or substitution editing gene expression mRNA modification RNA metabolic process primary metabolic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA modification macromolecule modification metabolic process cellular process macromolecule metabolic process cytidine to uridine editing base conversion or substitution editing gene expression nucleobase-containing compound biosynthetic process mRNA processing macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA processing regulation of cellular process 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 regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process DNA-templated transcription initiation regulation of gene expression positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050610	APOBEC Cytidine Deaminase	Family
A, B, C, D	IPR016193	Cytidine deaminase-like	Homologous Superfamily
A, B, C, D	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9Y235	gastric carcinoma Alzheimer disease psoriasis large cell medulloblastoma

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.