4DDG

Crystal structure of human OTUB1/UbcH5b~Ub/Ub

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000151	cellular_component	ubiquitin ligase complex
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	0019787	molecular_function	ubiquitin-like protein transferase 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	0000151	cellular_component	ubiquitin ligase complex
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	0019787	molecular_function	ubiquitin-like protein transferase 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	0000151	cellular_component	ubiquitin ligase complex
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	0019787	molecular_function	ubiquitin-like protein transferase 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	0000151	cellular_component	ubiquitin ligase complex
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	0019787	molecular_function	ubiquitin-like protein transferase 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	0000151	cellular_component	ubiquitin ligase complex
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	0019787	molecular_function	ubiquitin-like protein transferase 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	0000151	cellular_component	ubiquitin ligase complex
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	0019787	molecular_function	ubiquitin-like protein transferase 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	24
Details	SITE: Interacts with activating enzyme

Chain	Residue	Details
D	ARG54
H	ARG72
I	ARG54
I	ARG72
M	ARG54
M	ARG72
N	ARG54
N	ARG72
O	ARG54
O	ARG72
P	ARG54
D	ARG72
P	ARG72
Q	ARG54
Q	ARG72
R	ARG54
R	ARG72
E	ARG54
E	ARG72
F	ARG54
F	ARG72
G	ARG54
G	ARG72
H	ARG54

---

site_id	SWS_FT_FI2
Number of Residues	12
Details	SITE: Essential for function

Chain	Residue	Details
D	HIS68
P	HIS68
Q	HIS68
R	HIS68
E	HIS68
F	HIS68
G	HIS68
H	HIS68
I	HIS68
M	HIS68
N	HIS68
O	HIS68

---

site_id	SWS_FT_FI3
Number of Residues	12
Details	MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291

Chain	Residue	Details
D	SER65
P	SER65
Q	SER65
R	SER65
E	SER65
F	SER65
G	SER65
H	SER65
I	SER65
M	SER65
N	SER65
O	SER65

---

site_id	SWS_FT_FI4
Number of Residues	12
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457

Chain	Residue	Details
D	THR66
P	THR66
Q	THR66
R	THR66
E	THR66
F	THR66
G	THR66
H	THR66
I	THR66
M	THR66
N	THR66
O	THR66

---

site_id	SWS_FT_FI5
Number of Residues	12
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742

Chain	Residue	Details
D	GLY76
P	GLY76
Q	GLY76
R	GLY76
J	ILE1221
J	TYR1235
J	ASP1237
J	TYR1261
K	ILE1221
K	TYR1235
K	ASP1237
E	GLY76
K	TYR1261
L	ILE1221
L	TYR1235
L	ASP1237
L	TYR1261
F	GLY76
G	GLY76
H	GLY76
I	GLY76
M	GLY76
N	GLY76
O	GLY76

---

site_id	SWS_FT_FI6
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603

Chain	Residue	Details
D	LYS6
P	LYS6
Q	LYS6
R	LYS6
E	LYS6
F	LYS6
G	LYS6
H	LYS6
I	LYS6
M	LYS6
N	LYS6
O	LYS6

---

site_id	SWS_FT_FI7
Number of Residues	24
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
A	TYR1026
H	GLY76
I	GLY76
M	GLY76
N	GLY76
O	GLY76
D	GLY76
P	GLY76
Q	GLY76
R	GLY76
C	TYR1026
E	GLY76
K	TYR1026
F	GLY76
G	GLY76

---

site_id	SWS_FT_FI8
Number of Residues	24
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144

Chain	Residue	Details
D	LYS11
H	LYS48
I	LYS11
I	LYS48
M	LYS11
M	LYS48
N	LYS11
N	LYS48
O	LYS11
O	LYS48
P	LYS11
D	LYS48
P	LYS48
Q	LYS11
Q	LYS48
R	LYS11
R	LYS48
E	LYS11
E	LYS48
F	LYS11
F	LYS48
G	LYS11
G	LYS48
H	LYS11

---

site_id	SWS_FT_FI9
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860

Chain	Residue	Details
D	LYS27
P	LYS27
Q	LYS27
R	LYS27
E	LYS27
F	LYS27
G	LYS27
H	LYS27
I	LYS27
M	LYS27
N	LYS27
O	LYS27

---

site_id	SWS_FT_FI10
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127

Chain	Residue	Details
D	LYS29
P	LYS29
Q	LYS29
R	LYS29
E	LYS29
F	LYS29
G	LYS29
H	LYS29
I	LYS29
M	LYS29
N	LYS29
O	LYS29

---

site_id	SWS_FT_FI11
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577

Chain	Residue	Details
D	LYS33
P	LYS33
Q	LYS33
R	LYS33
E	LYS33
F	LYS33
G	LYS33
H	LYS33
I	LYS33
M	LYS33
N	LYS33
O	LYS33

---

site_id	SWS_FT_FI12
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106

Chain	Residue	Details
D	LYS63
P	LYS63
Q	LYS63
R	LYS63
E	LYS63
F	LYS63
G	LYS63
H	LYS63
I	LYS63
M	LYS63
N	LYS63
O	LYS63

---