Annotations: 5UDH

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	UBC-like	8034823	3000570	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	UBC-like	8034823	3000570	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RING/U-box like	8041693	3000160	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	RING/U-box like	8041693	3000160	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 [auth C]	PF00179	e5udhC1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
D	PF00179	e5udhD1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
E	PF00240	e5udhE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
A	PF21235	e5udhA1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: PF21235	ECOD (1.6)
A	PF19422	e5udhA5	A: alpha bundles	X: N-cbl like	H: C-terminal domain of E3 ubiquitin-protein ligase ARIH1 (From Topology)	T: C-terminal domain of E3 ubiquitin-protein ligase ARIH1	F: PF19422	ECOD (1.6)
A	PF13923	e5udhA3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13923	ECOD (1.6)
A	PF01485	e5udhA4	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: IBR domain	F: PF01485	ECOD (1.6)
A	PF22191	e5udhA2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: IBR domain	F: PF22191	ECOD (1.6)
C [auth B]	PF21235	e5udhB2	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: PF21235	ECOD (1.6)
C [auth B]	PF19422	e5udhB5	A: alpha bundles	X: N-cbl like	H: C-terminal domain of E3 ubiquitin-protein ligase ARIH1 (From Topology)	T: C-terminal domain of E3 ubiquitin-protein ligase ARIH1	F: PF19422	ECOD (1.6)
C [auth B]	PF13923	e5udhB3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13923	ECOD (1.6)
C [auth B]	PF01485	e5udhB1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: Ariadne-1 protein homolog	F: PF01485	ECOD (1.6)
C [auth B]	PF22191	e5udhB4	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: Ariadne-1 protein homolog	F: PF22191	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
D	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
A	1.20.120.1750	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
C [auth B]	1.20.120.1750	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D	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
E	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
A, C [auth B]	PF21235	E3 ubiquitin-protein ligase ARIH1, UBA-like domain (ARI1_UBAl)	E3 ubiquitin-protein ligase ARIH1, UBA-like domain	This entry represents the UBA-like (UBL) domain from the Human Homologue of Ariadne (HHARI) and its homologues, which are Ariadne subfamily E3 ubiquitin ligase proteins [1-4]. This domain binds to Ubiquitin and NEDD8 [3,4].	Domain
A, C [auth B]	PF00097	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4)	Zinc finger, C3HC4 type (RING finger)	The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many protein ...	The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many proteins containing a RING finger play a key role in the ubiquitination pathway [2].	Domain
A, C [auth B]	PF01485	IBR domain, a half RING-finger domain (IBR)	IBR domain, a half RING-finger domain	The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (Pfam:PF00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain [2]. Proteins that contain two Ring fing ...	The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (Pfam:PF00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain [2]. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription [3]. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease [3][4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D	Ubiquitin-conjugating enzyme E2 L3	ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding binding organic cyclic compound binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding	organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cell cycle phase transition cellular process cell cycle cell cycle process regulation of protein modification process regulation of catalytic activity organic substance metabolic process organonitrogen compound metabolic process macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cell cycle phase transition cellular process cell cycle cell cycle process regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process positive regulation of transferase activity regulation of post-translational protein modification regulation of protein metabolic process biological regulation positive regulation of catalytic activity regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cell population proliferation cellular response to stimulus response to organic substance response to stimulus response to lipid response to endogenous stimulus cellular response to organic cyclic compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to organic substance cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus protein localization regulation of localization establishment of protein localization cellular localization regulation of cellular process regulation of protein localization protein targeting regulation of protein targeting to mitochondrion positive regulation of establishment of protein localization localization cellular macromolecule localization positive regulation of protein targeting to mitochondrion positive regulation of cellular process regulation of establishment of protein localization establishment of localization regulation of establishment of protein localization to mitochondrion establishment of protein localization to organelle regulation of protein targeting regulation of cellular localization macromolecule localization protein localization to organelle protein localization to mitochondrion positive regulation of protein localization protein targeting to mitochondrion establishment of protein localization to mitochondrion positive regulation of establishment of protein localization to mitochondrion organonitrogen compound catabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process organic substance catabolic process protein polyubiquitination cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription protein K11-linked ubiquitination response to glucocorticoid cellular response to glucocorticoid stimulus cellular response to corticosteroid stimulus response to corticosteroid	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex
E	Ubiquitin C variant	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol 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
A, C [auth B]	E3 ubiquitin-protein ligase ARIH1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein conjugating enzyme binding protein binding binding enzyme binding ubiquitin conjugating enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein conjugating enzyme binding protein binding binding enzyme binding ubiquitin conjugating enzyme binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of metabolic process organic substance metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of metabolic process organic substance metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process organonitrogen compound catabolic process regulation of biological process organonitrogen compound metabolic process regulation of protein metabolic process biological regulation primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process organic substance catabolic process regulation of protein 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 protein polyubiquitination cellular response to stimulus regulation of cellular process response to stimulus signaling PKR/eIFalpha signaling integrated stress response signaling intracellular signal transduction cell communication cellular response to stress response to stress intracellular signaling cassette cellular process signal transduction	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen Cajal body nuclear body inclusion body Lewy body protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B [auth C], D	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
B [auth C], D	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
E	IPR019954	Ubiquitin conserved site	Conserved Site
E	IPR000626	Ubiquitin-like domain	Domain
E	IPR019956	Ubiquitin domain	Domain
E	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C [auth B]	IPR002867	IBR domain	Domain
A, C [auth B]	IPR044066	TRIAD supradomain	Domain
A, C [auth B]	IPR048962	E3 ubiquitin-protein ligase ARIH1-like, UBA-like domain	Domain
A, C [auth B]	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A, C [auth B]	IPR045840	Ariadne domain	Domain
A, C [auth B]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C [auth B]	IPR031127	E3 ubiquitin ligase RBR family	Family
A, C [auth B]	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], D	Pharos: P68036	Crohn disease juvenile idiopathic arthritis chronic hepatitis B virus infection atypical teratoid rhabdoid tumor myositis psoriasis tuberculosis celiac disease hepatitis B virus infection lung cancer osteosarcoma systemic lupus erythematosus inflammatory bowel disease malignant mesothelioma ovarian cancer Crohn disease juvenile idiopathic arthritis chronic hepatitis B virus infection atypical teratoid rhabdoid tumor myositis psoriasis tuberculosis celiac disease hepatitis B virus infection lung cancer osteosarcoma systemic lupus erythematosus inflammatory bowel disease malignant mesothelioma ovarian cancer systemic sclerosis
E	Pharos: 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
A, C [auth B]	Pharos: Q9Y4X5	atypical teratoid rhabdoid tumor malignant glioma Pick disease psoriasis glioblastoma osteosarcoma pilocytic astrocytoma spina bifida intellectual disability ovarian cancer plasma cell myeloma 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 R01GM133198.