Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3IHP

Covalent Ubiquitin-Usp5 Complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0002841	biological_process	negative regulation of T cell mediated immune response to tumor cell
A	0004197	molecular_function	cysteine-type endopeptidase activity
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005764	cellular_component	lysosome
A	0005829	cellular_component	cytosol
A	0006508	biological_process	proteolysis
A	0007346	biological_process	regulation of mitotic cell cycle
A	0008233	molecular_function	peptidase activity
A	0008234	molecular_function	cysteine-type peptidase activity
A	0008270	molecular_function	zinc ion binding
A	0010494	cellular_component	cytoplasmic stress granule
A	0016567	biological_process	protein ubiquitination
A	0016579	biological_process	protein deubiquitination
A	0016787	molecular_function	hydrolase activity
A	0031647	biological_process	regulation of protein stability
A	0032435	biological_process	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
A	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
A	0043130	molecular_function	ubiquitin binding
A	0045727	biological_process	positive regulation of translation
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
A	0050868	biological_process	negative regulation of T cell activation
A	0071108	biological_process	protein K48-linked deubiquitination
A	0098793	cellular_component	presynapse
A	0101005	molecular_function	deubiquitinase activity
A	0140251	biological_process	regulation protein catabolic process at presynapse
A	1901800	biological_process	positive regulation of proteasomal protein catabolic process
A	2000059	biological_process	negative regulation of ubiquitin-dependent protein catabolic process
B	0002841	biological_process	negative regulation of T cell mediated immune response to tumor cell
B	0004197	molecular_function	cysteine-type endopeptidase activity
B	0004843	molecular_function	cysteine-type deubiquitinase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005764	cellular_component	lysosome
B	0005829	cellular_component	cytosol
B	0006508	biological_process	proteolysis
B	0007346	biological_process	regulation of mitotic cell cycle
B	0008233	molecular_function	peptidase activity
B	0008234	molecular_function	cysteine-type peptidase activity
B	0008270	molecular_function	zinc ion binding
B	0010494	cellular_component	cytoplasmic stress granule
B	0016567	biological_process	protein ubiquitination
B	0016579	biological_process	protein deubiquitination
B	0016787	molecular_function	hydrolase activity
B	0031647	biological_process	regulation of protein stability
B	0032435	biological_process	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
B	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
B	0043130	molecular_function	ubiquitin binding
B	0045727	biological_process	positive regulation of translation
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0046872	molecular_function	metal ion binding
B	0050868	biological_process	negative regulation of T cell activation
B	0071108	biological_process	protein K48-linked deubiquitination
B	0098793	cellular_component	presynapse
B	0101005	molecular_function	deubiquitinase activity
B	0140251	biological_process	regulation protein catabolic process at presynapse
B	1901800	biological_process	positive regulation of proteasomal protein catabolic process
B	2000059	biological_process	negative regulation of ubiquitin-dependent protein catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NEH C 76

Chain	Residue
A	ASN333
A	CYS335
A	GLN433
A	GLY794
C	GLY75

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NEH D 76

Chain	Residue
D	GLY75
B	ASN333
B	CYS335
B	GLN433
B	GLY794

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL D 77

Chain	Residue
D	ARG74

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 836

Chain	Residue
A	CYS199
A	CYS202
A	CYS219
A	HIS232

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 836

Chain	Residue
B	CYS199
B	CYS202
B	CYS219
B	HIS232

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	LYS27-ASP52

site_id	PS00972
Number of Residues	16
Details	USP_1 Ubiquitin specific protease (USP) domain signature 1. GIrnlGNsCYLNSvVQ

Chain	Residue	Details
A	GLY327-GLN342

site_id	PS00973
Number of Residues	19
Details	USP_2 Ubiquitin specific protease (USP) domain signature 2. YqLfAFisHmGtstmc.GHY

Chain	Residue	Details
A	TYR778-TYR796

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	80
Details	Domain: {"description":"UBA 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00212","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Active site: {"description":"Nucleophile"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU10092","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10093","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00502","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	11
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"N-acetylalanine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"39900921","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	108
Details	Zinc finger: {"description":"UBP-type; degenerate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00502","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Site: {"description":"Interacts with activating enzyme"}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Site: {"description":"Essential for function"}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
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_FI13
Number of Residues	2
Details	Modified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	4
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_FI16
Number of Residues	4
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_FI17
Number of Residues	2
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_FI18
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":"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_FI19
Number of Residues	2
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)