4DHI

Structure of C. elegans OTUB1 bound to human UBC13

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 [auth B]	d4dhib_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	nematode (Caenorhabditis elegans ) [TaxId: 6239 ],	SCOPe (2.08)
B [auth D]	d4dhid_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	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 [auth B]	SCOP2B Superfamily	Cysteine proteinases	8088202	3001808	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	UBC-like	8034195	3000570	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 [auth B]	OTU	e4dhiB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: OTU	ECOD (1.6)
B [auth D]	UQ_con	e4dhiD1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.30.200.60	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A [auth B]	1.20.1300.20	Mainly Alpha	Up-down Bundle	3 helical TM bundles of succinate and fumarate reductases	Peptidase C65 Otubain, subdomain 2	CATH (4.3.0)
B [auth D]	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Ubiquitin thioesterase otubain-like	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity protein binding binding ubiquitin binding ubiquitin-like protein binding	protein deubiquitination primary metabolic process protein modification by small protein removal macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal proteolysis	cell periphery cellular anatomical structure plasma membrane membrane
B [auth D]	Ubiquitin-conjugating enzyme E2 N	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 protein binding binding ubiquitin binding ubiquitin-like protein binding RNA 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 ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process DNA repair double-strand break repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process positive regulation of double-strand break repair nucleic acid metabolic process regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus DNA damage response metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA double-strand break processing positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response regulation protein catabolic process at synapse catabolic process regulation of catabolic process regulation protein catabolic process at postsynapse protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process postreplication repair protein polyubiquitination positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription protein K63-linked ubiquitination biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism innate immune response antiviral innate immune response response to external biotic stimulus response to virus DNA recombination recombinational repair double-strand break repair via homologous recombination negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of cell communication negative regulation of TORC1 signaling negative regulation of TOR signaling negative regulation of cellular process regulation of TORC1 signaling TOR signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction TORC1 signaling regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of protein K63-linked ubiquitination positive regulation of protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein K63-linked ubiquitination positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of protein polyubiquitination regulation of post-translational protein modification regulation of protein metabolic process positive regulation of protein polyubiquitination protein monoubiquitination	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen protein-containing complex synapse cell junction glutamatergic synapse ubiquitin conjugating enzyme complex catalytic complex transferase complex intracellular protein-containing complex UBC13-MMS2 complex postsynapse ubiquitin ligase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR016615	Ubiquitin thioesterase Otubain	Family
A [auth B]	IPR042467	Peptidase C65, otubain, subdomain 2	Homologous Superfamily
A [auth B]	IPR003323	OTU domain	Domain
A [auth B]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A [auth B]	IPR019400	Peptidase C65, otubain	Family
A [auth B]	IPR042468	Peptidase C65, otubain, subdomain 1	Homologous Superfamily
B [auth D]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B [auth D]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
B [auth D]	IPR000608	Ubiquitin-conjugating enzyme E2, catalytic core domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth D]	Pharos: P61088	Embryo Loss astrocytic tumor lymphoplasmacytic lymphoma osteosarcoma pituitary cancer invasive ductal breast carcinoma malignant ependymoma ovarian cancer psoriasis lung cancer oligodendroglioma Pick disease 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 R01GM157729.