5SXG | pdb_00005sxg

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	d5sxgb1	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	d5sxgb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5sxga1	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)
A	d5sxga2	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)
B	SCOP2B Superfamily	Cytidine deaminase-like	8105523	3001838	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytidine deaminase-like	8105523	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)
B	SBP_bac_1	e5sxgB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SBP_bac_1	ECOD (v294.1)
A	Spa1_C	e5sxgA1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F: Spa1_C	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA dC->dU-editing enzyme APOBEC-3B	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 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 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 nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of viral genome replication nucleobase-containing compound biosynthetic process single stranded viral RNA replication via double stranded DNA intermediate regulation of viral process regulation of viral life cycle viral genome replication regulation of viral genome replication negative regulation of RNA metabolic process defense response to virus response to virus 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 membrane-enclosed lumen 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 membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

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: Q9UH17	squamous cell carcinoma urinary bladder cancer breast carcinoma cervical cancer Neoplastic Processes cancer head and neck cancer psoriasis urinary bladder neoplasm benign neoplasm IgA glomerulonephritis malignant tumor of neck neoplasm of neck non-small cell lung carcinoma breast cancer squamous cell carcinoma urinary bladder cancer breast carcinoma cervical cancer Neoplastic Processes cancer head and neck cancer psoriasis urinary bladder neoplasm benign neoplasm IgA glomerulonephritis malignant tumor of neck neoplasm of neck non-small cell lung carcinoma breast cancer head and neck neoplasm lung adenocarcinoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.