Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2YHO

The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000166	molecular_function	nucleotide binding
B	0000209	biological_process	protein polyubiquitination
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	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0030514	biological_process	negative regulation of BMP signaling pathway
B	0031398	biological_process	positive regulation of protein ubiquitination
B	0032991	cellular_component	protein-containing complex
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0061630	molecular_function	ubiquitin protein ligase activity
B	0061631	molecular_function	ubiquitin conjugating enzyme activity
B	0070936	biological_process	protein K48-linked ubiquitination
B	1904262	biological_process	negative regulation of TORC1 signaling
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000166	molecular_function	nucleotide binding
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	0005737	cellular_component	cytoplasm
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	0030514	biological_process	negative regulation of BMP signaling pathway
D	0031398	biological_process	positive regulation of protein ubiquitination
D	0032991	cellular_component	protein-containing complex
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0061630	molecular_function	ubiquitin protein ligase activity
D	0061631	molecular_function	ubiquitin conjugating enzyme activity
D	0070936	biological_process	protein K48-linked ubiquitination
D	1904262	biological_process	negative regulation of TORC1 signaling
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0000166	molecular_function	nucleotide binding
F	0000209	biological_process	protein polyubiquitination
F	0004842	molecular_function	ubiquitin-protein transferase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006511	biological_process	ubiquitin-dependent protein catabolic process
F	0016567	biological_process	protein ubiquitination
F	0016740	molecular_function	transferase activity
F	0030514	biological_process	negative regulation of BMP signaling pathway
F	0031398	biological_process	positive regulation of protein ubiquitination
F	0032991	cellular_component	protein-containing complex
F	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
F	0061630	molecular_function	ubiquitin protein ligase activity
F	0061631	molecular_function	ubiquitin conjugating enzyme activity
F	0070936	biological_process	protein K48-linked ubiquitination
F	1904262	biological_process	negative regulation of TORC1 signaling
H	0000122	biological_process	negative regulation of transcription by RNA polymerase II
H	0000166	molecular_function	nucleotide binding
H	0000209	biological_process	protein polyubiquitination
H	0004842	molecular_function	ubiquitin-protein transferase activity
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006511	biological_process	ubiquitin-dependent protein catabolic process
H	0016567	biological_process	protein ubiquitination
H	0016740	molecular_function	transferase activity
H	0030514	biological_process	negative regulation of BMP signaling pathway
H	0031398	biological_process	positive regulation of protein ubiquitination
H	0032991	cellular_component	protein-containing complex
H	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
H	0061630	molecular_function	ubiquitin protein ligase activity
H	0061631	molecular_function	ubiquitin conjugating enzyme activity
H	0070936	biological_process	protein K48-linked ubiquitination
H	1904262	biological_process	negative regulation of TORC1 signaling

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1001

Chain	Residue
A	CYS387
A	CYS390
A	CYS408
A	CYS411

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1002

Chain	Residue
A	CYS402
A	HIS404
A	CYS418
A	CYS421

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 1001

Chain	Residue
C	CYS390
C	CYS408
C	CYS411
F	GLY-1
C	CYS387

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 1002

Chain	Residue
C	CYS402
C	HIS404
C	CYS418
C	CYS421

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 1001

Chain	Residue
E	CYS387
E	CYS390
E	CYS408
E	CYS411

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 1002

Chain	Residue
E	CYS402
E	HIS404
E	CYS418
E	CYS421

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN G 1001

Chain	Residue
G	CYS387
G	CYS390
G	CYS408
G	CYS411

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN G 1002

Chain	Residue
G	CYS402
G	HIS404
G	CYS418
G	CYS421

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT H 1148

Chain	Residue
H	ILE67
H	ILE84
H	HOH2034

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT G 1442

Chain	Residue
G	GLU383
G	ALA384
G	LEU386
G	MET388
G	HOH2024

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT H 1149

Chain	Residue
H	ARG5
H	LYS8

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT B 1148

Chain	Residue
B	ILE67
B	ILE84
B	HOH2041

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT F 1148

Chain	Residue
F	ILE67
F	SER83
F	ILE84

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT B 1149

Chain	Residue
B	PHE69
B	THR70
B	SER80
B	GLY82
B	HOH2043

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT A 1439

Chain	Residue
A	GLU383
A	ALA384
A	LEU386
A	HOH2010

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT H 1150

Chain	Residue
D	SER105
D	SER108
H	PRO57
H	THR58

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ACT A 1440

Chain	Residue
A	HIS404

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
B	TYR74-LEU89

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	140
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	Region: {"description":"Critical for homodimerization"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	584
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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