Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4DHJ

The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub 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	0005634	cellular_component	nucleus
A	0005886	cellular_component	plasma membrane
A	0006508	biological_process	proteolysis
A	0008233	molecular_function	peptidase activity
A	0008234	molecular_function	cysteine-type peptidase activity
A	0016579	biological_process	protein deubiquitination
A	0016787	molecular_function	hydrolase activity
A	0043130	molecular_function	ubiquitin binding
C	0000151	cellular_component	ubiquitin ligase complex
C	0000166	molecular_function	nucleotide binding
C	0000209	biological_process	protein polyubiquitination
C	0000724	biological_process	double-strand break repair via homologous recombination
C	0000729	biological_process	DNA double-strand break processing
C	0003723	molecular_function	RNA binding
C	0004842	molecular_function	ubiquitin-protein transferase 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	0006282	biological_process	regulation of DNA repair
C	0006301	biological_process	postreplication repair
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006974	biological_process	DNA damage response
C	0016567	biological_process	protein ubiquitination
C	0016740	molecular_function	transferase activity
C	0019787	molecular_function	ubiquitin-like protein transferase activity
C	0031371	cellular_component	ubiquitin conjugating enzyme complex
C	0031372	cellular_component	UBC13-MMS2 complex
C	0031625	molecular_function	ubiquitin protein ligase binding
C	0032991	cellular_component	protein-containing complex
C	0033182	biological_process	obsolete regulation of histone ubiquitination
C	0035370	cellular_component	UBC13-UEV1A complex
C	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
C	0043130	molecular_function	ubiquitin binding
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0045739	biological_process	positive regulation of DNA repair
C	0050852	biological_process	T cell receptor signaling pathway
C	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
C	0061631	molecular_function	ubiquitin conjugating enzyme activity
C	0070062	cellular_component	extracellular exosome
C	0070534	biological_process	protein K63-linked ubiquitination
C	0097027	molecular_function	ubiquitin-protein transferase activator activity
C	0140374	biological_process	antiviral innate immune response
C	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
C	1902533	biological_process	positive regulation of intracellular signal transduction
C	1904262	biological_process	negative regulation of TORC1 signaling
C	2000781	biological_process	positive regulation of double-strand break repair
E	0004843	molecular_function	cysteine-type deubiquitinase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005886	cellular_component	plasma membrane
E	0006508	biological_process	proteolysis
E	0008233	molecular_function	peptidase activity
E	0008234	molecular_function	cysteine-type peptidase activity
E	0016579	biological_process	protein deubiquitination
E	0016787	molecular_function	hydrolase activity
E	0043130	molecular_function	ubiquitin binding
G	0000151	cellular_component	ubiquitin ligase complex
G	0000166	molecular_function	nucleotide binding
G	0000209	biological_process	protein polyubiquitination
G	0000724	biological_process	double-strand break repair via homologous recombination
G	0000729	biological_process	DNA double-strand break processing
G	0003723	molecular_function	RNA binding
G	0004842	molecular_function	ubiquitin-protein transferase activity
G	0005515	molecular_function	protein binding
G	0005524	molecular_function	ATP binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006281	biological_process	DNA repair
G	0006282	biological_process	regulation of DNA repair
G	0006301	biological_process	postreplication repair
G	0006511	biological_process	ubiquitin-dependent protein catabolic process
G	0006974	biological_process	DNA damage response
G	0016567	biological_process	protein ubiquitination
G	0016740	molecular_function	transferase activity
G	0019787	molecular_function	ubiquitin-like protein transferase activity
G	0031371	cellular_component	ubiquitin conjugating enzyme complex
G	0031372	cellular_component	UBC13-MMS2 complex
G	0031625	molecular_function	ubiquitin protein ligase binding
G	0032991	cellular_component	protein-containing complex
G	0033182	biological_process	obsolete regulation of histone ubiquitination
G	0035370	cellular_component	UBC13-UEV1A complex
G	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
G	0043130	molecular_function	ubiquitin binding
G	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
G	0045739	biological_process	positive regulation of DNA repair
G	0050852	biological_process	T cell receptor signaling pathway
G	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
G	0061631	molecular_function	ubiquitin conjugating enzyme activity
G	0070062	cellular_component	extracellular exosome
G	0070534	biological_process	protein K63-linked ubiquitination
G	0097027	molecular_function	ubiquitin-protein transferase activator activity
G	0140374	biological_process	antiviral innate immune response
G	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
G	1902533	biological_process	positive regulation of intracellular signal transduction
G	1904262	biological_process	negative regulation of TORC1 signaling
G	2000781	biological_process	positive regulation of double-strand break repair
I	0004843	molecular_function	cysteine-type deubiquitinase activity
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005886	cellular_component	plasma membrane
I	0006508	biological_process	proteolysis
I	0008233	molecular_function	peptidase activity
I	0008234	molecular_function	cysteine-type peptidase activity
I	0016579	biological_process	protein deubiquitination
I	0016787	molecular_function	hydrolase activity
I	0043130	molecular_function	ubiquitin binding
K	0000151	cellular_component	ubiquitin ligase complex
K	0000166	molecular_function	nucleotide binding
K	0000209	biological_process	protein polyubiquitination
K	0000724	biological_process	double-strand break repair via homologous recombination
K	0000729	biological_process	DNA double-strand break processing
K	0003723	molecular_function	RNA binding
K	0004842	molecular_function	ubiquitin-protein transferase 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	0006282	biological_process	regulation of DNA repair
K	0006301	biological_process	postreplication repair
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0006974	biological_process	DNA damage response
K	0016567	biological_process	protein ubiquitination
K	0016740	molecular_function	transferase activity
K	0019787	molecular_function	ubiquitin-like protein transferase activity
K	0031371	cellular_component	ubiquitin conjugating enzyme complex
K	0031372	cellular_component	UBC13-MMS2 complex
K	0031625	molecular_function	ubiquitin protein ligase binding
K	0032991	cellular_component	protein-containing complex
K	0033182	biological_process	obsolete regulation of histone ubiquitination
K	0035370	cellular_component	UBC13-UEV1A complex
K	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
K	0043130	molecular_function	ubiquitin binding
K	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
K	0045739	biological_process	positive regulation of DNA repair
K	0050852	biological_process	T cell receptor signaling pathway
K	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
K	0061631	molecular_function	ubiquitin conjugating enzyme activity
K	0070062	cellular_component	extracellular exosome
K	0070534	biological_process	protein K63-linked ubiquitination
K	0097027	molecular_function	ubiquitin-protein transferase activator activity
K	0140374	biological_process	antiviral innate immune response
K	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
K	1902533	biological_process	positive regulation of intracellular signal transduction
K	1904262	biological_process	negative regulation of TORC1 signaling
K	2000781	biological_process	positive regulation of double-strand break repair
L	0004843	molecular_function	cysteine-type deubiquitinase activity
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005886	cellular_component	plasma membrane
L	0006508	biological_process	proteolysis
L	0008233	molecular_function	peptidase activity
L	0008234	molecular_function	cysteine-type peptidase activity
L	0016579	biological_process	protein deubiquitination
L	0016787	molecular_function	hydrolase activity
L	0043130	molecular_function	ubiquitin binding
N	0000151	cellular_component	ubiquitin ligase complex
N	0000166	molecular_function	nucleotide binding
N	0000209	biological_process	protein polyubiquitination
N	0000724	biological_process	double-strand break repair via homologous recombination
N	0000729	biological_process	DNA double-strand break processing
N	0003723	molecular_function	RNA binding
N	0004842	molecular_function	ubiquitin-protein transferase activity
N	0005515	molecular_function	protein binding
N	0005524	molecular_function	ATP binding
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005737	cellular_component	cytoplasm
N	0005829	cellular_component	cytosol
N	0006281	biological_process	DNA repair
N	0006282	biological_process	regulation of DNA repair
N	0006301	biological_process	postreplication repair
N	0006511	biological_process	ubiquitin-dependent protein catabolic process
N	0006974	biological_process	DNA damage response
N	0016567	biological_process	protein ubiquitination
N	0016740	molecular_function	transferase activity
N	0019787	molecular_function	ubiquitin-like protein transferase activity
N	0031371	cellular_component	ubiquitin conjugating enzyme complex
N	0031372	cellular_component	UBC13-MMS2 complex
N	0031625	molecular_function	ubiquitin protein ligase binding
N	0032991	cellular_component	protein-containing complex
N	0033182	biological_process	obsolete regulation of histone ubiquitination
N	0035370	cellular_component	UBC13-UEV1A complex
N	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
N	0043130	molecular_function	ubiquitin binding
N	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
N	0045739	biological_process	positive regulation of DNA repair
N	0050852	biological_process	T cell receptor signaling pathway
N	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
N	0061631	molecular_function	ubiquitin conjugating enzyme activity
N	0070062	cellular_component	extracellular exosome
N	0070534	biological_process	protein K63-linked ubiquitination
N	0097027	molecular_function	ubiquitin-protein transferase activator activity
N	0140374	biological_process	antiviral innate immune response
N	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
N	1902533	biological_process	positive regulation of intracellular signal transduction
N	1904262	biological_process	negative regulation of TORC1 signaling
N	2000781	biological_process	positive 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	LYS527-ASP552
B	LYS527-ASP552

site_id	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNVdkl.GrICLdiL

Chain	Residue	Details
C	TYR76-LEU91

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	SITE: Interacts with activating enzyme

Chain	Residue	Details
B	ARG554
B	ARG572
F	ARG554
F	ARG572
J	ARG554
J	ARG572
M	ARG554
M	ARG572

site_id	SWS_FT_FI2
Number of Residues	4
Details	SITE: Essential for function

Chain	Residue	Details
B	HIS568
F	HIS568
J	HIS568
M	HIS568

site_id	SWS_FT_FI3
Number of Residues	4
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
G	LYS92
N	LYS92
B	SER565
F	SER565
J	SER565
M	SER565

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269\|PubMed:32330457

Chain	Residue	Details
M	THR566
J	THR566
B	THR566
F	THR566

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269\|PubMed:28525742

Chain	Residue	Details
B	GLZ576
F	GLZ576
J	GLZ576
M	GLZ576

site_id	SWS_FT_FI6
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603

Chain	Residue	Details
M	LYS506
B	LYS506
J	LYS506
F	LYS506

site_id	SWS_FT_FI7
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
B	GLZ576
F	GLZ576
J	GLZ576
M	GLZ576

site_id	SWS_FT_FI8
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603, ECO:0000269\|PubMed:16543144

Chain	Residue	Details
J	LYS511
J	LYS548
M	LYS511
M	LYS548
B	LYS511
B	LYS548
F	LYS511
F	LYS548

site_id	SWS_FT_FI9
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305\|PubMed:15466860

Chain	Residue	Details
B	LYS527
F	LYS527
J	LYS527
M	LYS527

site_id	SWS_FT_FI10
Number of Residues	4
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
B	LYS529
F	LYS529
J	LYS529
M	LYS529

site_id	SWS_FT_FI11
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:25752577

Chain	Residue	Details
B	LYS533
F	LYS533
J	LYS533
M	LYS533

site_id	SWS_FT_FI12
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16543144, ECO:0000269\|PubMed:18719106

Chain	Residue	Details
B	LYS563
F	LYS563
J	LYS563
M	LYS563

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