5YJ0 | pdb_00005yj0

Mouse Cereblon thalidomide binding domain complexed with S-form thalidomide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
P [auth t]	Yippee-Mis18_1	e5yj0t1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
O [auth q]	Yippee-Mis18_1	e5yj0q1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
N [auth n]	Yippee-Mis18_1	e5yj0n1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
M [auth k]	Yippee-Mis18_1	e5yj0k1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
L [auth h]	Yippee-Mis18_1	e5yj0h1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
K [auth e]	Yippee-Mis18_1	e5yj0e1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
J [auth b]	Yippee-Mis18_1	e5yj0b1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
I [auth Y]	Yippee-Mis18_1	e5yj0Y1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
H [auth V]	Yippee-Mis18_1	e5yj0V1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
G [auth S]	Yippee-Mis18_1	e5yj0S1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
F [auth P]	Yippee-Mis18_1	e5yj0P1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
E [auth M]	Yippee-Mis18_1	e5yj0M1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
D [auth J]	Yippee-Mis18_1	e5yj0J1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
C [auth G]	Yippee-Mis18_1	e5yj0G1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
B [auth D]	Yippee-Mis18_1	e5yj0D1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)
A	Yippee-Mis18_1	e5yj0A1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P [auth t]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
O [auth q]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
N [auth n]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
M [auth k]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
L [auth h]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
K [auth e]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
J [auth b]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
I [auth Y]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
H [auth V]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
G [auth S]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
F [auth P]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
E [auth M]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
D [auth J]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
C [auth G]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
B [auth D]	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
A	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V], I [auth Y], J [auth b], K [auth e], L [auth h], M [auth k], N [auth n], O [auth q], P [auth t]	PF03226	Yippee zinc-binding/DNA-binding /Mis18, centromere assembly (Yippee-Mis18)	Yippee zinc-binding/DNA-binding /Mis18, centromere assembly	This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of ...	This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus [5]. This entry also includes the CULT domain proteins such as Cereblon [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V], I [auth Y], J [auth b], K [auth e], L [auth h], M [auth k], N [auth n], O [auth q], P [auth t]	Protein cereblon	protein binding binding transmembrane transporter binding cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway biological regulation regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis regulation of localization regulation of potassium ion transport negative regulation of ion transmembrane transporter activity negative regulation of potassium ion transmembrane transporter activity transport monoatomic ion transmembrane transport negative regulation of monoatomic ion transport negative regulation of biological process potassium ion transmembrane transport regulation of transmembrane transporter activity negative regulation of transport regulation of monoatomic ion transmembrane transport metal ion transport negative regulation of transmembrane transport monoatomic cation transmembrane transport localization negative regulation of monoatomic ion transmembrane transport negative regulation of cellular process monoatomic ion transport negative regulation of cation transmembrane transport monoatomic cation transport regulation of metal ion transport negative regulation of potassium ion transport negative regulation of large conductance calcium-activated potassium channel activity regulation of transport regulation of monoatomic ion transport negative regulation of transporter activity negative regulation of molecular function negative regulation of potassium ion transmembrane transport regulation of potassium ion transmembrane transport establishment of localization transmembrane transport regulation of molecular function regulation of transmembrane transport potassium ion transport regulation of monoatomic cation transmembrane transport primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal negative regulation of cellular component organization negative regulation of protein-containing complex assembly catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process behavior multicellular organismal process locomotory behavior exploration behavior locomotory exploration behavior	cellular anatomical structure membrane intracellular anatomical structure perinuclear region of cytoplasm cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex membrane-bounded organelle cellular anatomical structure membrane intracellular anatomical structure perinuclear region of cytoplasm cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V], I [auth Y], J [auth b], K [auth e], L [auth h], M [auth k], N [auth n], O [auth q], P [auth t]	IPR015947	PUA-like superfamily	Homologous Superfamily
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V], I [auth Y], J [auth b], K [auth e], L [auth h], M [auth k], N [auth n], O [auth q], P [auth t]	IPR046336	Lon protease, N-terminal domain superfamily	Homologous Superfamily
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V], I [auth Y], J [auth b], K [auth e], L [auth h], M [auth k], N [auth n], O [auth q], P [auth t]	IPR004910	Yippee/Mis18/Cereblon	Domain
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V], I [auth Y], J [auth b], K [auth e], L [auth h], M [auth k], N [auth n], O [auth q], P [auth t]	IPR003111	Lon protease, N-terminal domain	Domain
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V], I [auth Y], J [auth b], K [auth e], L [auth h], M [auth k], N [auth n], O [auth q], P [auth t]	IPR034750	CULT domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.