Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1XD3

Crystal structure of UCHL3-UbVME complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
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	0016567	biological_process	protein ubiquitination
A	0016579	biological_process	protein deubiquitination
A	0016787	molecular_function	hydrolase activity
A	0019784	molecular_function	deNEDDylase activity
A	0030163	biological_process	protein catabolic process
A	0043130	molecular_function	ubiquitin binding
A	0043687	biological_process	post-translational protein modification
A	0101005	molecular_function	deubiquitinase activity
C	0004843	molecular_function	cysteine-type deubiquitinase activity
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006508	biological_process	proteolysis
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0008233	molecular_function	peptidase activity
C	0008234	molecular_function	cysteine-type peptidase activity
C	0016567	biological_process	protein ubiquitination
C	0016579	biological_process	protein deubiquitination
C	0016787	molecular_function	hydrolase activity
C	0019784	molecular_function	deNEDDylase activity
C	0030163	biological_process	protein catabolic process
C	0043130	molecular_function	ubiquitin binding
C	0043687	biological_process	post-translational protein modification
C	0101005	molecular_function	deubiquitinase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 2001

Chain	Residue
A	HOH2246
C	ASP163
C	HOH2129
C	HOH2193
C	HOH2366

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 2002

Chain	Residue
C	HOH2194
C	HOH2281
A	HOH2123
A	HOH2191
A	HOH2227
C	HOH2150

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 2003

Chain	Residue
C	HIS179
C	HOH2184
C	HOH2185
C	HOH2191
C	HOH2270
C	HOH2374

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MG C 2004

Chain	Residue
C	MG2005
C	HOH2065
C	HOH2072
C	HOH2169
C	HOH2190
C	HOH2249
C	HOH2397
C	HOH2425

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG C 2005

Chain	Residue
C	GLN78
C	ASP79
C	MG2004
C	HOH2169
C	HOH2181
C	HOH2190
C	HOH2249

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 2006

Chain	Residue
A	LYS108
A	ASP109
A	HOH2346
B	HOH1243

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG C 2007

Chain	Residue
C	GLU149
C	HOH2069
C	HOH2078
C	HOH2433

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG C 2008

Chain	Residue
C	ASP79
C	THR81
C	TYR181

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 2009

Chain	Residue
A	HOH2264
A	HOH2305
D	HOH2344
D	HOH2347
D	HOH2354

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 2010

Chain	Residue
A	LYS21
A	GLY24
A	LEU25
A	GLU114

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GVE B 1176

Chain	Residue
A	ILE58
A	GLN89
A	ASN93
A	CYS95
A	VAL166
A	LEU168
A	HIS169
B	GLY75

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GVE D 2276

Chain	Residue
C	GLN89
C	ASN93
C	CYS95
C	VAL166
C	LEU168
C	HIS169
C	HOH2432
D	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. QtisNACGtigLIHAIA

Chain	Residue	Details
A	GLN89-ALA105

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	448
Details	Domain: {"description":"UCH catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	20
Details	Region: {"description":"Interaction with ubiquitin","evidences":[{"source":"PubMed","id":"15531586","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	14
Details	Region: {"description":"Interaction with ubiquitin. Crossover loop which restricts access of large ubiquitin adducts to the active site","evidences":[{"source":"PubMed","id":"15531586","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19047059","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19154770","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20380862","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9790970","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Active site: {"description":"Proton donor","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Site: {"description":"Transition state stabilizer","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Site: {"description":"Important for enzyme activity","evidences":[{"source":"PROSITE-ProRule","id":"PRU01393","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	4
Details	Annotated By Reference To The Literature 1uch

Chain	Residue	Details
A	CYS95
A	HIS169
A	ASP184
A	GLN89

site_id	CSA2
Number of Residues	4
Details	Annotated By Reference To The Literature 1uch

Chain	Residue	Details
C	CYS95
C	HIS169
C	ASP184
C	GLN89

site_id	MCSA1
Number of Residues	4
Details	M-CSA 597

Chain	Residue	Details
A	GLN89	electrostatic stabiliser
A	CYS95	covalent catalysis, proton shuttle (general acid/base)
A	HIS169	proton shuttle (general acid/base)
A	ASP184	electrostatic stabiliser

site_id	MCSA2
Number of Residues	4
Details	M-CSA 597

Chain	Residue	Details
C	GLN89	electrostatic stabiliser
C	CYS95	covalent catalysis, proton shuttle (general acid/base)
C	HIS169	proton shuttle (general acid/base)
C	ASP184	electrostatic stabiliser

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