4DDG

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
J	0000166	molecular_function	nucleotide binding
J	0000209	biological_process	protein polyubiquitination
J	0002250	biological_process	adaptive immune response
J	0002376	biological_process	immune system process
J	0004842	molecular_function	ubiquitin-protein transferase activity
J	0004843	molecular_function	cysteine-type deubiquitinase activity
J	0005515	molecular_function	protein binding
J	0005524	molecular_function	ATP binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006281	biological_process	DNA repair
J	0006508	biological_process	proteolysis
J	0006511	biological_process	ubiquitin-dependent protein catabolic process
J	0006974	biological_process	DNA damage response
J	0008233	molecular_function	peptidase activity
J	0008234	molecular_function	cysteine-type peptidase activity
J	0016567	biological_process	protein ubiquitination
J	0016579	biological_process	protein deubiquitination
J	0016740	molecular_function	transferase activity
J	0016787	molecular_function	hydrolase activity
J	0019784	molecular_function	deNEDDylase activity
J	0031625	molecular_function	ubiquitin protein ligase binding
J	0032991	cellular_component	protein-containing complex
J	0036211	biological_process	protein modification process
J	0043130	molecular_function	ubiquitin binding
J	0051865	biological_process	protein autoubiquitination
J	0055105	molecular_function	ubiquitin-protein transferase inhibitor activity
J	0061630	molecular_function	ubiquitin protein ligase activity
J	0061631	molecular_function	ubiquitin conjugating enzyme activity
J	0070062	cellular_component	extracellular exosome
J	0070936	biological_process	protein K48-linked ubiquitination
J	0071108	biological_process	protein K48-linked deubiquitination
J	1904263	biological_process	positive regulation of TORC1 signaling
J	2000780	biological_process	negative regulation of double-strand break repair
K	0000166	molecular_function	nucleotide binding
K	0000209	biological_process	protein polyubiquitination
K	0002250	biological_process	adaptive immune response
K	0002376	biological_process	immune system process
K	0004842	molecular_function	ubiquitin-protein transferase activity
K	0004843	molecular_function	cysteine-type deubiquitinase activity
K	0005515	molecular_function	protein binding
K	0005524	molecular_function	ATP binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006281	biological_process	DNA repair
K	0006508	biological_process	proteolysis
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0006974	biological_process	DNA damage response
K	0008233	molecular_function	peptidase activity
K	0008234	molecular_function	cysteine-type peptidase activity
K	0016567	biological_process	protein ubiquitination
K	0016579	biological_process	protein deubiquitination
K	0016740	molecular_function	transferase activity
K	0016787	molecular_function	hydrolase activity
K	0019784	molecular_function	deNEDDylase activity
K	0031625	molecular_function	ubiquitin protein ligase binding
K	0032991	cellular_component	protein-containing complex
K	0036211	biological_process	protein modification process
K	0043130	molecular_function	ubiquitin binding
K	0051865	biological_process	protein autoubiquitination
K	0055105	molecular_function	ubiquitin-protein transferase inhibitor activity
K	0061630	molecular_function	ubiquitin protein ligase activity
K	0061631	molecular_function	ubiquitin conjugating enzyme activity
K	0070062	cellular_component	extracellular exosome
K	0070936	biological_process	protein K48-linked ubiquitination
K	0071108	biological_process	protein K48-linked deubiquitination
K	1904263	biological_process	positive regulation of TORC1 signaling
K	2000780	biological_process	negative regulation of double-strand break repair
L	0000166	molecular_function	nucleotide binding
L	0000209	biological_process	protein polyubiquitination
L	0002250	biological_process	adaptive immune response
L	0002376	biological_process	immune system process
L	0004842	molecular_function	ubiquitin-protein transferase activity
L	0004843	molecular_function	cysteine-type deubiquitinase activity
L	0005515	molecular_function	protein binding
L	0005524	molecular_function	ATP binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0006281	biological_process	DNA repair
L	0006508	biological_process	proteolysis
L	0006511	biological_process	ubiquitin-dependent protein catabolic process
L	0006974	biological_process	DNA damage response
L	0008233	molecular_function	peptidase activity
L	0008234	molecular_function	cysteine-type peptidase activity
L	0016567	biological_process	protein ubiquitination
L	0016579	biological_process	protein deubiquitination
L	0016740	molecular_function	transferase activity
L	0016787	molecular_function	hydrolase activity
L	0019784	molecular_function	deNEDDylase activity
L	0031625	molecular_function	ubiquitin protein ligase binding
L	0032991	cellular_component	protein-containing complex
L	0036211	biological_process	protein modification process
L	0043130	molecular_function	ubiquitin binding
L	0051865	biological_process	protein autoubiquitination
L	0055105	molecular_function	ubiquitin-protein transferase inhibitor activity
L	0061630	molecular_function	ubiquitin protein ligase activity
L	0061631	molecular_function	ubiquitin conjugating enzyme activity
L	0070062	cellular_component	extracellular exosome
L	0070936	biological_process	protein K48-linked ubiquitination
L	0071108	biological_process	protein K48-linked deubiquitination
L	1904263	biological_process	positive regulation of TORC1 signaling
L	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	876
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	6
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	1146
Details	Domain: {"description":"OTU","evidences":[{"source":"PROSITE-ProRule","id":"PRU00139","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	96
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	114
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	42
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	6
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	6
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	6
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	24
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	6
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	6
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	900
Details	Domain: {"description":"Ubiquitin-like 9","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---