Annotations: 3K9O

The crystal structure of E2-25K and UBB+1 complex

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)
A	d3k9oa2	All alpha proteins	RuvA C-terminal domain-like	UBA-like	UBA domain	Ubiquitin-conjugating enzyme E2-25 kDa, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3k9oa1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin-conjugating enzyme E2-25 kDa, E2 domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3k9ob_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	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	UBC-like	8041006	3000570	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBA-like	8041004	3001235	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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	Alpha_adaptinC2	e3k9oA1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Alpha_adaptinC2	ECOD (v295.2)
B	Alpha_adaptinC2	e3k9oB1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Alpha_adaptinC2	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00627	UBA/TS-N domain (UBA)	UBA/TS-N domain	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin a ...	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle [1]. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU [2]. The domain has been found in non EF-TS proteins such as alpha-NAC Swiss:P70670 and MJ0280 Swiss:Q57728 [1].	Domain
A	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain
B	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ubiquitin-conjugating enzyme E2 K	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity ubiquitin protein ligase binding protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus positive regulation of cell communication regulation of cellular process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway biological regulation response to peptide regulation of response to cytokine stimulus regulation of response to stimulus response to chemical regulation of cell communication response to tumor necrosis factor positive regulation of cytokine-mediated signaling pathway positive regulation of signaling protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein K48-linked ubiquitination positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-threonine phosphorylation positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of peptidyl-threonine phosphorylation phosphorylation regulation of protein metabolic process regulation of macromolecule metabolic process regulation of phosphorylation regulation of metabolic process peptidyl-threonine phosphorylation protein polymerization protein-containing complex organization homeostatic process free ubiquitin chain polymerization cellular component organization cellular component biogenesis cellular component assembly cellular homeostasis protein-containing complex assembly cellular component organization or biogenesis ubiquitin recycling positive regulation of response to biotic stimulus regulation of type I interferon-mediated signaling pathway response to biotic stimulus interferon-mediated signaling pathway cellular response to type I interferon positive regulation of immune response regulation of immune system process positive regulation of immune system process immune response response to other organism regulation of innate immune response response to external stimulus defense response to other organism positive regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of type I interferon-mediated signaling pathway positive regulation of response to external stimulus regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of innate immune response defense response defense response to symbiont immune system process type I interferon-mediated signaling pathway cellular response to interferon-beta response to interferon-beta	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol filopodium tip intracellular membraneless organelle actin cytoskeleton plasma membrane bounded cell projection intracellular organelle cell projection actin-based cell projection cytoskeleton organelle membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol filopodium tip intracellular membraneless organelle actin cytoskeleton plasma membrane bounded cell projection intracellular organelle cell projection actin-based cell projection cytoskeleton organelle membraneless organelle filopodium membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	Ubiquitin	protein tag activity molecular tag activity RNA binding binding nucleic acid binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle cytosolic ribosome membraneless organelle intracellular membraneless organelle ribosome cytosol extracellular region extracellular exosome extracellular vesicle extracellular organelle extracellular membrane-bounded organelle endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
A	IPR009060	UBA-like superfamily	Homologous Superfamily
A	IPR042599	Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain	Domain
A	IPR015940	Ubiquitin-associated domain	Domain
B	IPR019954	Ubiquitin conserved site	Conserved Site
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR019956	Ubiquitin domain	Domain
B	IPR050158	Ubiquitin and ubiquitin-like	Family
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: P61086	astrocytic tumor lung cancer myopathy subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor malignant ependymoma ovarian cancer glioblastoma malignant glioma plasma cell myeloma
B	: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer