Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5AIT

A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008270	molecular_function	zinc ion binding
B	0000151	cellular_component	ubiquitin ligase complex
B	0000166	molecular_function	nucleotide binding
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	0006513	biological_process	protein monoubiquitination
B	0006974	biological_process	DNA damage response
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	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	0031669	biological_process	cellular response to nutrient levels
B	0032991	cellular_component	protein-containing complex
B	0038202	biological_process	TORC1 signaling
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	0000209	biological_process	protein polyubiquitination
D	0000729	biological_process	DNA double-strand break processing
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0006282	biological_process	regulation of DNA repair
D	0006301	biological_process	postreplication repair
D	0016567	biological_process	protein ubiquitination
D	0031371	cellular_component	ubiquitin conjugating enzyme complex
D	0031372	cellular_component	UBC13-MMS2 complex
D	0042275	biological_process	error-free postreplication DNA repair
D	0070062	cellular_component	extracellular exosome
D	0070534	biological_process	protein K63-linked ubiquitination
D	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
D	2000781	biological_process	positive regulation of double-strand break repair
E	0000151	cellular_component	ubiquitin ligase complex
E	0000166	molecular_function	nucleotide binding
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	0006513	biological_process	protein monoubiquitination
E	0006974	biological_process	DNA damage response
E	0016567	biological_process	protein ubiquitination
E	0016740	molecular_function	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	0031669	biological_process	cellular response to nutrient levels
E	0032991	cellular_component	protein-containing complex
E	0038202	biological_process	TORC1 signaling
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
G	0000209	biological_process	protein polyubiquitination
G	0000729	biological_process	DNA double-strand break processing
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005737	cellular_component	cytoplasm
G	0006282	biological_process	regulation of DNA repair
G	0006301	biological_process	postreplication repair
G	0016567	biological_process	protein ubiquitination
G	0031371	cellular_component	ubiquitin conjugating enzyme complex
G	0031372	cellular_component	UBC13-MMS2 complex
G	0042275	biological_process	error-free postreplication DNA repair
G	0070062	cellular_component	extracellular exosome
G	0070534	biological_process	protein K63-linked ubiquitination
G	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
G	2000781	biological_process	positive regulation of double-strand break repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 1260

Chain	Residue
A	CYS136
A	CYS139
A	ARG151
A	CYS163
A	CYS166

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1261

Chain	Residue
A	CYS158
A	HIS160
A	CYS177
A	CYS180

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1262

Chain	Residue
A	CYS201
A	CYS204
A	CYS228
A	CYS231

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1263

Chain	Residue
A	CYS223
A	HIS225
A	CYS242
A	CYS245

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. CgHvFCsqCL

Chain	Residue	Details
A	CYS158-LEU167
A	CYS223-LEU232

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	45
Details	Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20681948","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3NG2","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15)","evidences":[{"source":"PubMed","id":"16112642","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16122702","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	135
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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