Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5VNZ

Structure of a TRAF6-Ubc13~Ub complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0005164	molecular_function	tumor necrosis factor receptor binding
A	0016567	biological_process	protein ubiquitination
A	0046872	molecular_function	metal ion binding
B	0000151	cellular_component	ubiquitin ligase complex
B	0000209	biological_process	protein polyubiquitination
B	0000724	biological_process	double-strand break repair via homologous recombination
B	0000729	biological_process	DNA double-strand break processing
B	0003723	molecular_function	RNA binding
B	0004842	molecular_function	ubiquitin-protein transferase 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	0006282	biological_process	regulation of DNA repair
B	0006301	biological_process	postreplication repair
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0019787	molecular_function	ubiquitin-like protein transferase activity
B	0031371	cellular_component	ubiquitin conjugating enzyme complex
B	0031372	cellular_component	UBC13-MMS2 complex
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0032991	cellular_component	protein-containing complex
B	0033182	biological_process	obsolete regulation of histone ubiquitination
B	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
B	0043130	molecular_function	ubiquitin binding
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0045739	biological_process	positive regulation of DNA repair
B	0050852	biological_process	T cell receptor signaling pathway
B	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
B	0061631	molecular_function	ubiquitin conjugating enzyme activity
B	0070062	cellular_component	extracellular exosome
B	0070534	biological_process	protein K63-linked ubiquitination
B	0097027	molecular_function	ubiquitin-protein transferase activator activity
B	0140374	biological_process	antiviral innate immune response
B	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
B	1902533	biological_process	positive regulation of intracellular signal transduction
B	1904262	biological_process	negative regulation of TORC1 signaling
B	2000781	biological_process	positive regulation of double-strand break repair
D	0004842	molecular_function	ubiquitin-protein transferase activity
D	0005164	molecular_function	tumor necrosis factor receptor binding
D	0016567	biological_process	protein ubiquitination
D	0046872	molecular_function	metal ion binding
E	0000151	cellular_component	ubiquitin ligase complex
E	0000209	biological_process	protein polyubiquitination
E	0000724	biological_process	double-strand break repair via homologous recombination
E	0000729	biological_process	DNA double-strand break processing
E	0003723	molecular_function	RNA binding
E	0004842	molecular_function	ubiquitin-protein transferase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006281	biological_process	DNA repair
E	0006282	biological_process	regulation of DNA repair
E	0006301	biological_process	postreplication repair
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0016567	biological_process	protein ubiquitination
E	0016740	molecular_function	transferase activity
E	0019787	molecular_function	ubiquitin-like protein transferase activity
E	0031371	cellular_component	ubiquitin conjugating enzyme complex
E	0031372	cellular_component	UBC13-MMS2 complex
E	0031625	molecular_function	ubiquitin protein ligase binding
E	0032991	cellular_component	protein-containing complex
E	0033182	biological_process	obsolete regulation of histone ubiquitination
E	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
E	0043130	molecular_function	ubiquitin binding
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0045739	biological_process	positive regulation of DNA repair
E	0050852	biological_process	T cell receptor signaling pathway
E	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
E	0061631	molecular_function	ubiquitin conjugating enzyme activity
E	0070062	cellular_component	extracellular exosome
E	0070534	biological_process	protein K63-linked ubiquitination
E	0097027	molecular_function	ubiquitin-protein transferase activator activity
E	0140374	biological_process	antiviral innate immune response
E	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
E	1902533	biological_process	positive regulation of intracellular signal transduction
E	1904262	biological_process	negative regulation of TORC1 signaling
E	2000781	biological_process	positive regulation of double-strand break repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 201

Chain	Residue
A	CYS71
A	CYS74
A	CYS91
A	CYS94

site_id	AC2
Number of Residues	5
Details	binding site for residue ZN A 202

Chain	Residue
A	CYS86
A	HIS88
A	CYS106
A	VAL108
A	ASP109

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN A 203

Chain	Residue
A	CYS135
A	CYS140
A	HIS152
A	CYS156

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN D 201

Chain	Residue
D	CYS71
D	CYS74
D	CYS91
D	CYS94

site_id	AC5
Number of Residues	5
Details	binding site for residue ZN D 202

Chain	Residue
D	CYS86
D	HIS88
D	CYS106
D	VAL108
D	ASP109

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN D 203

Chain	Residue
D	CYS135
D	CYS140
D	HIS152
D	CYS156

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	PS00518
Number of Residues	10
Details	ZF_RING_1 Zinc finger RING-type signature. CgHrFCdsCI

Chain	Residue	Details
A	CYS86-ILE95

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	78
Details	ZN_FING: RING-type; degenerate => ECO:0000255\|PROSITE-ProRule:PRU00175

Chain	Residue	Details
A	CYS71-ASN110
D	CYS71-ASN110
F	ARG54
F	ARG72

site_id	SWS_FT_FI2
Number of Residues	2
Details	SITE: Essential for function

Chain	Residue	Details
C	HIS68
F	HIS68

site_id	SWS_FT_FI3
Number of Residues	2
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
C	SER65
F	SER65
E	THR92

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269\|PubMed:32330457

Chain	Residue	Details
C	THR66
F	THR66

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269\|PubMed:28525742

Chain	Residue	Details
C	GLY76
F	GLY76

site_id	SWS_FT_FI6
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603

Chain	Residue	Details
C	LYS6
F	LYS6

site_id	SWS_FT_FI7
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
C	GLY76
F	GLY76

site_id	SWS_FT_FI8
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16443603, ECO:0000269\|PubMed:16543144

Chain	Residue	Details
C	LYS11
C	LYS48
F	LYS11
F	LYS48

site_id	SWS_FT_FI9
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305\|PubMed:15466860

Chain	Residue	Details
C	LYS27
F	LYS27

site_id	SWS_FT_FI10
Number of Residues	2
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
C	LYS29
F	LYS29

site_id	SWS_FT_FI11
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:25752577

Chain	Residue	Details
C	LYS33
F	LYS33

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:16543144, ECO:0000269\|PubMed:18719106

Chain	Residue	Details
C	LYS63
F	LYS63

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