4DM9

The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OMe)-FMK

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	d4dm9a_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Ubiquitin carboxyl-terminal hydrolase UCH-L	Ubiquitin carboxyl-terminal hydrolase isozyme l1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4dm9b_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Ubiquitin carboxyl-terminal hydrolase UCH-L	Ubiquitin carboxyl-terminal hydrolase isozyme l1	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	Cysteine proteinases	8040164	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8040164	3001808	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	Peptidase_C12	e4dm9A1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C12	ECOD (1.6)
B	Peptidase_C12	e4dm9B1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.532.10	Alpha Beta	3-Layer(aba) Sandwich	Ubiquitin C-terminal Hydrolase UCH-l3	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	CATH (4.3.0)
B	3.40.532.10	Alpha Beta	3-Layer(aba) Sandwich	Ubiquitin C-terminal Hydrolase UCH-l3	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01088	Ubiquitin carboxyl-terminal hydrolase, family 1 (Peptidase_C12)	Ubiquitin carboxyl-terminal hydrolase, family 1	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ubiquitin carboxyl-terminal hydrolase isozyme L1	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity adrenergic receptor binding signaling receptor binding G protein-coupled receptor binding alpha-2A adrenergic receptor binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport axonal transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated axo-dendritic transport mitochondrion transport along microtubule organelle localization establishment of localization in cell establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport axonal transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated axo-dendritic transport mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process axonal transport of mitochondrion regulation of biological process catabolic process regulation of cellular process macroautophagy cellular metabolic process biological regulation autophagy regulation of cellular metabolic process regulation of catabolic process regulation of autophagy cellular catabolic process regulation of macroautophagy regulation of cellular catabolic process metabolic process regulation of metabolic process process utilizing autophagic mechanism cellular response to stimulus response to stimulus regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of signal transduction regulation of transferase activity regulation of MAP kinase activity intracellular signal transduction negative regulation of cellular metabolic process regulation of primary metabolic process cell communication negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process intracellular signaling cassette negative regulation of protein modification process signal transduction phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of MAPK cascade regulation of molecular function regulation of kinase activity regulation of response to stimulus negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process macromolecule metabolic process regulation of protein modification process regulation of protein phosphorylation signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphate metabolic process negative regulation of cell communication organic substance metabolic process regulation of intracellular signal transduction negative regulation of protein serine/threonine kinase activity negative regulation of cellular process protein metabolic process negative regulation of macromolecule metabolic process regulation of signaling organonitrogen compound metabolic process negative regulation of response to stimulus negative regulation of molecular function negative regulation of MAP kinase activity regulation of protein kinase activity regulation of macromolecule metabolic process negative regulation of protein kinase activity negative regulation of signal transduction negative regulation of phosphorus metabolic process MAPK cascade regulation of cell communication regulation of phosphorylation negative regulation of phosphorylation negative regulation of MAPK cascade response to stress response to ischemia behavior multicellular organismal process eating behavior feeding behavior system process nervous system process neuromuscular process organonitrogen compound catabolic process 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 organic substance catabolic process germ cell proliferation cell population proliferation sexual reproduction reproductive process multicellular organismal reproductive process male germ cell proliferation gamete generation axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization axon target recognition nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cellular response to chemical stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus protein deubiquitination protein modification by small protein removal post-translational protein modification protein modification by small protein conjugation or removal adult walking behavior adult locomotory behavior adult behavior locomotory behavior walking behavior muscle structure development muscle cell development muscle cell differentiation	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 organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cell projection neuron projection terminus neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body neuronal cell body neuron projection cytoplasm axon axon cytoplasm cytoplasmic region plasma membrane bounded cell projection cytoplasm
C [auth X], D [auth Y]	Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR001578	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	Domain
A, B	IPR036959	Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P09936	early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome non-small cell lung carcinoma Parkinson disease 5, autosomal dominant, susceptibility to Parkinson disease hereditary spastic paraplegia gallbladder cancer peripheral nervous system disease neurodegenerative disease peripheral neuropathy esophageal cancer lung adenocarcinoma malignant colon neoplasm medulloblastoma acute myeloid leukemia ovarian cancer early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome non-small cell lung carcinoma Parkinson disease 5, autosomal dominant, susceptibility to Parkinson disease hereditary spastic paraplegia gallbladder cancer peripheral nervous system disease neurodegenerative disease peripheral neuropathy esophageal cancer lung adenocarcinoma malignant colon neoplasm medulloblastoma acute myeloid leukemia ovarian cancer Ataxias, Hereditary pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer cystic fibrosis Pick disease head and neck cancer large cell medulloblastoma lung cancer malignant ependymoma neoplasm of esophagus oligodendroglioma adenoma pancreatic intraductal papillary-mucinous carcinoma atopic eczema paraplegia chronic obstructive pulmonary disease diabetes mellitus Emery-Dreifuss muscular dystrophy pilocytic astrocytoma gallbladder neoplasm hepatocellular carcinoma lung carcinoma malignant glioma osteosarcoma astrocytic tumor pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor congenital diaphragmatic hernia psoriasis glioblastoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.