Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5H7S

Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000151	cellular_component	ubiquitin ligase complex
A	0000209	biological_process	protein polyubiquitination
A	0000724	biological_process	double-strand break repair via homologous recombination
A	0000729	biological_process	DNA double-strand break processing
A	0003723	molecular_function	RNA binding
A	0004842	molecular_function	ubiquitin-protein transferase 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	0006282	biological_process	regulation of DNA repair
A	0006301	biological_process	postreplication repair
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006513	biological_process	protein monoubiquitination
A	0016567	biological_process	protein ubiquitination
A	0016740	molecular_function	transferase activity
A	0019787	molecular_function	ubiquitin-like protein transferase activity
A	0031371	cellular_component	ubiquitin conjugating enzyme complex
A	0031372	cellular_component	UBC13-MMS2 complex
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0032991	cellular_component	protein-containing complex
A	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
A	0043130	molecular_function	ubiquitin binding
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0045739	biological_process	positive regulation of DNA repair
A	0050852	biological_process	T cell receptor signaling pathway
A	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
A	0061631	molecular_function	ubiquitin conjugating enzyme activity
A	0070062	cellular_component	extracellular exosome
A	0070534	biological_process	protein K63-linked ubiquitination
A	0097027	molecular_function	ubiquitin-protein transferase activator activity
A	0140374	biological_process	antiviral innate immune response
A	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
A	1902533	biological_process	positive regulation of intracellular signal transduction
A	1904262	biological_process	negative regulation of TORC1 signaling
A	2000781	biological_process	positive regulation of double-strand break repair
B	0046872	molecular_function	metal ion binding
C	0000151	cellular_component	ubiquitin ligase complex
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	0006513	biological_process	protein monoubiquitination
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	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
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

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

Chain	Residue
D	CYS4
D	CYS7
D	HIS11
D	HIS17

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN D 202

Chain	Residue
D	CYS31
D	CYS34
D	CYS51
D	CYS54

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

Chain	Residue
D	HIS48
D	CYS65
D	ASP68
D	CYS46

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN D 204

Chain	Residue
D	CYS95
D	CYS101
D	HIS113
D	CYS118

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN B 201

Chain	Residue
B	CYS4
B	CYS7
B	HIS11
B	HIS17

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN B 202

Chain	Residue
B	CYS31
B	CYS34
B	CYS51
B	CYS54

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN B 203

Chain	Residue
B	CYS46
B	HIS48
B	CYS65
B	ASP68

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN B 204

Chain	Residue
B	CYS95
B	CYS101
B	HIS113
B	CYS118

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
E	LYS27-ASP52

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

Chain	Residue	Details
D	CYS46-LEU55

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: Glycyl thioester intermediate => ECO:0000255\|PROSITE-ProRule:PRU00388

Chain	Residue	Details
A	LYS87
C	LYS87
F	ARG54
F	ARG72

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS82
C	LYS82

site_id	SWS_FT_FI3
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15) => ECO:0000269\|PubMed:16112642, ECO:0000269\|PubMed:16122702

Chain	Residue	Details
A	ALA92
F	SER65
C	ALA92

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

Chain	Residue	Details
E	THR66
F	THR66

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

Chain	Residue	Details
E	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
E	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
E	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
E	LYS11
E	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
E	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
E	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
E	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
E	LYS63
F	LYS63

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