Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3IFW

Crystal structure of the S18Y variant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004197	molecular_function	cysteine-type endopeptidase activity
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0005515	molecular_function	protein binding
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005789	cellular_component	endoplasmic reticulum membrane
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006508	biological_process	proteolysis
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0008233	molecular_function	peptidase activity
A	0008234	molecular_function	cysteine-type peptidase activity
A	0008242	molecular_function	omega peptidase activity
A	0016241	biological_process	regulation of macroautophagy
A	0016579	biological_process	protein deubiquitination
A	0016787	molecular_function	hydrolase activity
A	0030163	biological_process	protein catabolic process
A	0030424	cellular_component	axon
A	0030547	molecular_function	signaling receptor inhibitor activity
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0031694	molecular_function	alpha-2A adrenergic receptor binding
A	0043022	molecular_function	ribosome binding
A	0043025	cellular_component	neuronal cell body
A	0043130	molecular_function	ubiquitin binding
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0043409	biological_process	negative regulation of MAPK cascade
A	0044306	cellular_component	neuron projection terminus
A	0045821	biological_process	positive regulation of glycolytic process
A	0071466	biological_process	cellular response to xenobiotic stimulus

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GVE B 76

Chain	Residue
A	LEU55
A	GLN84
A	ASN88
A	CYS90
A	PHE160
B	GLY75

Functional Information from PROSITE/UniProt

site_id	PS00140
Number of Residues	17
Details	UCH_1 Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. QtigNSCGtigLIHAVA

Chain	Residue	Details
A	GLN84-ALA100

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
B	LYS27-ASP52

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Propeptide: {"description":"Removed in mature form","featureId":"PRO_0000414311","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	219
Details	Domain: {"description":"UCH catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	10
Details	Region: {"description":"Interaction with ubiquitin","evidences":[{"source":"PubMed","id":"20439756","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	1
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20439756","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	1
Details	Active site: {"description":"Proton donor","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20439756","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	6
Details	Site: {"description":"Susceptible to oxidation","evidences":[{"source":"PubMed","id":"14722078","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	1
Details	Site: {"description":"Transition state stabilizer","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"8639624","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	1
Details	Site: {"description":"Important for enzyme activity","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	1
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"37316325","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q00981","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	1
Details	Lipidation: {"description":"S-farnesyl cysteine","evidences":[{"source":"PubMed","id":"19261853","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Site: {"description":"Interacts with activating enzyme"}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	1
Details	Site: {"description":"Essential for function"}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	1
Details	Modified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)