Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4DDI

Crystal structure of human OTUB1/UbcH5b~Ub/Ub

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000209	biological_process	protein polyubiquitination
A	0002250	biological_process	adaptive immune response
A	0002376	biological_process	immune system process
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006281	biological_process	DNA repair
A	0006508	biological_process	proteolysis
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006974	biological_process	DNA damage response
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	0016740	molecular_function	transferase activity
A	0016787	molecular_function	hydrolase activity
A	0019784	molecular_function	deNEDDylase activity
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0032991	cellular_component	protein-containing complex
A	0036211	biological_process	protein modification process
A	0043130	molecular_function	ubiquitin binding
A	0051865	biological_process	protein autoubiquitination
A	0055105	molecular_function	ubiquitin-protein transferase inhibitor activity
A	0061630	molecular_function	ubiquitin protein ligase activity
A	0061631	molecular_function	ubiquitin conjugating enzyme activity
A	0070062	cellular_component	extracellular exosome
A	0070936	biological_process	protein K48-linked ubiquitination
A	0071108	biological_process	protein K48-linked deubiquitination
A	1904263	biological_process	positive regulation of TORC1 signaling
A	2000780	biological_process	negative regulation of double-strand break repair
B	0000166	molecular_function	nucleotide binding
B	0000209	biological_process	protein polyubiquitination
B	0002250	biological_process	adaptive immune response
B	0002376	biological_process	immune system process
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0004843	molecular_function	cysteine-type deubiquitinase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006281	biological_process	DNA repair
B	0006508	biological_process	proteolysis
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0006974	biological_process	DNA damage response
B	0008233	molecular_function	peptidase activity
B	0008234	molecular_function	cysteine-type peptidase activity
B	0016567	biological_process	protein ubiquitination
B	0016579	biological_process	protein deubiquitination
B	0016740	molecular_function	transferase activity
B	0016787	molecular_function	hydrolase activity
B	0019784	molecular_function	deNEDDylase activity
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0032991	cellular_component	protein-containing complex
B	0036211	biological_process	protein modification process
B	0043130	molecular_function	ubiquitin binding
B	0051865	biological_process	protein autoubiquitination
B	0055105	molecular_function	ubiquitin-protein transferase inhibitor activity
B	0061630	molecular_function	ubiquitin protein ligase activity
B	0061631	molecular_function	ubiquitin conjugating enzyme activity
B	0070062	cellular_component	extracellular exosome
B	0070936	biological_process	protein K48-linked ubiquitination
B	0071108	biological_process	protein K48-linked deubiquitination
B	1904263	biological_process	positive regulation of TORC1 signaling
B	2000780	biological_process	negative regulation of double-strand break repair
C	0000166	molecular_function	nucleotide binding
C	0000209	biological_process	protein polyubiquitination
C	0002250	biological_process	adaptive immune response
C	0002376	biological_process	immune system process
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0004843	molecular_function	cysteine-type deubiquitinase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006281	biological_process	DNA repair
C	0006508	biological_process	proteolysis
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006974	biological_process	DNA damage response
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	0016740	molecular_function	transferase activity
C	0016787	molecular_function	hydrolase activity
C	0019784	molecular_function	deNEDDylase activity
C	0031625	molecular_function	ubiquitin protein ligase binding
C	0032991	cellular_component	protein-containing complex
C	0036211	biological_process	protein modification process
C	0043130	molecular_function	ubiquitin binding
C	0051865	biological_process	protein autoubiquitination
C	0055105	molecular_function	ubiquitin-protein transferase inhibitor activity
C	0061630	molecular_function	ubiquitin protein ligase activity
C	0061631	molecular_function	ubiquitin conjugating enzyme activity
C	0070062	cellular_component	extracellular exosome
C	0070936	biological_process	protein K48-linked ubiquitination
C	0071108	biological_process	protein K48-linked deubiquitination
C	1904263	biological_process	positive regulation of TORC1 signaling
C	2000780	biological_process	negative regulation of double-strand break repair

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
D	LYS27-ASP52

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	438
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	3
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	573
Details	Domain: {"description":"OTU","evidences":[{"source":"PROSITE-ProRule","id":"PRU00139","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	48
Details	Region: {"description":"Ubiquitin-conjugating enzyme E2 binding","evidences":[{"source":"PubMed","id":"22325355","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	57
Details	Region: {"description":"Free ubiquitin binding","evidences":[{"source":"PubMed","id":"22325355","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22367539","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4DHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	21
Details	Region: {"description":"Ubiquitin-conjugating enzyme E2 binding","evidences":[{"source":"PubMed","id":"22325355","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22367539","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4DHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	3
Details	Active site: {"evidences":[{"source":"PubMed","id":"22367539","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4DHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	3
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"22325355","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18954305","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	3
Details	Active site: {"evidences":[{"source":"PubMed","id":"22325355","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18954305","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	12
Details	Site: {"description":"Interacts with free ubiquitin","evidences":[{"source":"PubMed","id":"22325355","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	3
Details	Site: {"description":"Interacts with free ubiquitin","evidences":[{"source":"PubMed","id":"22325355","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22367539","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4DHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	3
Details	Modified residue: {"description":"Phosphotyrosine; by SRC","evidences":[{"source":"PubMed","id":"35927303","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	450
Details	Domain: {"description":"Ubiquitin-like 9","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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