Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5EDV

Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0008270	molecular_function	zinc ion binding
A	0071797	cellular_component	LUBAC complex
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0008270	molecular_function	zinc ion binding
B	0071797	cellular_component	LUBAC complex
C	0000151	cellular_component	ubiquitin ligase complex
C	0000209	biological_process	protein polyubiquitination
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	0005829	cellular_component	cytosol
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0016567	biological_process	protein ubiquitination
C	0016740	molecular_function	transferase 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	0051865	biological_process	protein autoubiquitination
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
D	0000151	cellular_component	ubiquitin ligase complex
D	0000209	biological_process	protein polyubiquitination
D	0004842	molecular_function	ubiquitin-protein transferase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005829	cellular_component	cytosol
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0016567	biological_process	protein ubiquitination
D	0016740	molecular_function	transferase activity
D	0019787	molecular_function	ubiquitin-like protein transferase activity
D	0031625	molecular_function	ubiquitin protein ligase binding
D	0032991	cellular_component	protein-containing complex
D	0036211	biological_process	protein modification process
D	0051865	biological_process	protein autoubiquitination
D	0061630	molecular_function	ubiquitin protein ligase activity
D	0061631	molecular_function	ubiquitin conjugating enzyme activity
D	0070062	cellular_component	extracellular exosome
D	0070936	biological_process	protein K48-linked ubiquitination
I	0000151	cellular_component	ubiquitin ligase complex
I	0000209	biological_process	protein polyubiquitination
I	0004842	molecular_function	ubiquitin-protein transferase activity
I	0005515	molecular_function	protein binding
I	0005524	molecular_function	ATP binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005829	cellular_component	cytosol
I	0006511	biological_process	ubiquitin-dependent protein catabolic process
I	0016567	biological_process	protein ubiquitination
I	0016740	molecular_function	transferase activity
I	0019787	molecular_function	ubiquitin-like protein transferase activity
I	0031625	molecular_function	ubiquitin protein ligase binding
I	0032991	cellular_component	protein-containing complex
I	0036211	biological_process	protein modification process
I	0051865	biological_process	protein autoubiquitination
I	0061630	molecular_function	ubiquitin protein ligase activity
I	0061631	molecular_function	ubiquitin conjugating enzyme activity
I	0070062	cellular_component	extracellular exosome
I	0070936	biological_process	protein K48-linked ubiquitination

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN A 2001

Chain	Residue
A	CYS699
A	VAL701
A	CYS702
A	CYS722
A	CYS725

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 2002

Chain	Residue
A	CYS717
A	CYS719
A	CYS744
A	CYS747

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN A 2003

Chain	Residue
A	CYS799
A	CYS802
A	CYS817
A	CYS820

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN A 2004

Chain	Residue
A	CYS825
A	CYS828
A	HIS836
A	CYS841

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN A 2005

Chain	Residue
A	CYS871
A	CYS874
A	CYS890
A	CYS893

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN A 2006

Chain	Residue
A	CYS898
A	CYS901
A	HIS926
A	CYS930

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN A 2007

Chain	Residue
A	CYS911
A	CYS916
A	HIS923
A	HIS925

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN A 2008

Chain	Residue
A	CYS969
A	CYS986
A	CYS998
A	HIS1001

site_id	AC9
Number of Residues	5
Details	binding site for residue ZN B 2001

Chain	Residue
B	CYS699
B	VAL701
B	CYS702
B	CYS722
B	CYS725

site_id	AD1
Number of Residues	4
Details	binding site for residue ZN B 2002

Chain	Residue
B	CYS717
B	CYS719
B	CYS744
B	CYS747

site_id	AD2
Number of Residues	4
Details	binding site for residue ZN B 2003

Chain	Residue
B	CYS799
B	CYS802
B	CYS817
B	CYS820

site_id	AD3
Number of Residues	4
Details	binding site for residue ZN B 2004

Chain	Residue
B	CYS825
B	CYS828
B	HIS836
B	CYS841

site_id	AD4
Number of Residues	4
Details	binding site for residue ZN B 2005

Chain	Residue
B	CYS871
B	CYS874
B	CYS890
B	CYS893

site_id	AD5
Number of Residues	4
Details	binding site for residue ZN B 2006

Chain	Residue
B	CYS898
B	CYS901
B	HIS926
B	CYS930

site_id	AD6
Number of Residues	4
Details	binding site for residue ZN B 2007

Chain	Residue
B	CYS911
B	CYS916
B	HIS923
B	HIS925

site_id	AD7
Number of Residues	4
Details	binding site for residue ZN B 2008

Chain	Residue
B	CYS969
B	CYS986
B	CYS998
B	HIS1001

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. CrHqFCsgCY

Chain	Residue	Details
A	CYS893-TYR902

Functional Information from SwissProt/UniProt

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

Chain	Residue	Details
E	ARG54
E	ARG72
F	ARG54
F	ARG72
G	ARG54
G	ARG72
H	ARG54
H	ARG72

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

Chain	Residue	Details
E	HIS68
F	HIS68
G	HIS68
H	HIS68

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
E	SER65
F	SER65
G	SER65
H	SER65

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

Chain	Residue	Details
E	THR66
F	THR66
G	THR66
H	THR66

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

Chain	Residue	Details
E	GLY76
F	GLY76
G	GLY76
H	GLY76
B	CYS699
B	CYS702
B	CYS722
B	CYS725

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
E	LYS6
F	LYS6
G	LYS6
H	LYS6
B	CYS717
B	CYS719
B	CYS744
B	CYS747

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
A	CYS799
A	CYS874
A	CYS890
A	CYS893
A	CYS898
A	CYS901
A	CYS916
A	HIS925
B	CYS799
B	CYS802
B	CYS817
E	GLY76
B	CYS820
B	CYS825
B	CYS828
B	HIS836
B	CYS841
B	CYS871
B	CYS874
B	CYS890
B	CYS893
B	CYS898
A	CYS817
B	CYS901
B	CYS916
B	HIS925
F	GLY76
A	CYS825
G	GLY76
A	HIS836
H	GLY76
A	CYS871

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
E	LYS11
E	LYS48
F	LYS11
F	LYS48
G	LYS11
G	LYS48
H	LYS11
H	LYS48

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
E	LYS27
F	LYS27
G	LYS27
H	LYS27

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
E	LYS29
F	LYS29
G	LYS29
H	LYS29

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
E	LYS33
F	LYS33
G	LYS33
H	LYS33

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
E	LYS63
F	LYS63
G	LYS63
H	LYS63

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