5YJ1 | pdb_00005yj1

Mouse Cereblon thalidomide binding domain complexed with R-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)
B [auth D]	SAM_KSR1_N	e5yj1D1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
C [auth G]	SAM_KSR1_N	e5yj1G1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
F [auth P]	SAM_KSR1_N	e5yj1P1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
G [auth S]	SAM_KSR1_N	e5yj1S1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
P [auth t]	SAM_KSR1_N	e5yj1t1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
O [auth q]	SAM_KSR1_N	e5yj1q1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
N [auth n]	SAM_KSR1_N	e5yj1n1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
M [auth k]	SAM_KSR1_N	e5yj1k1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
L [auth h]	SAM_KSR1_N	e5yj1h1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
K [auth e]	SAM_KSR1_N	e5yj1e1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
J [auth b]	SAM_KSR1_N	e5yj1b1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
I [auth Y]	SAM_KSR1_N	e5yj1Y1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
H [auth V]	SAM_KSR1_N	e5yj1V1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
E [auth M]	SAM_KSR1_N	e5yj1M1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
D [auth J]	SAM_KSR1_N	e5yj1J1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
A	SAM_KSR1_N	e5yj1A1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth D]	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)
F [auth P]	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)
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)
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)
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	regulation of localization regulation of biological process regulation of cellular process transport regulation of transport negative regulation of monoatomic ion transport regulation of monoatomic ion transport monoatomic ion transmembrane transport biological regulation negative regulation of biological process negative regulation of transport regulation of monoatomic ion transmembrane transport establishment of localization negative regulation of transmembrane transport transmembrane transport regulation of localization regulation of biological process regulation of cellular process transport regulation of transport negative regulation of monoatomic ion transport regulation of monoatomic ion transport monoatomic ion transmembrane transport biological regulation negative regulation of biological process negative regulation of transport regulation of monoatomic ion transmembrane transport establishment of localization negative regulation of transmembrane transport transmembrane transport localization regulation of transmembrane transport negative regulation of monoatomic ion transmembrane transport negative regulation of cellular process monoatomic ion transport cellular process developmental process multicellular organism development multicellular organismal process limb development appendage development anatomical structure development cellular response to stimulus positive regulation of cell communication 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 signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication 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 potassium ion transport negative regulation of ion transmembrane transporter activity negative regulation of potassium ion transmembrane transporter activity potassium ion transmembrane transport regulation of transmembrane transporter activity metal ion transport monoatomic cation transmembrane 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 negative regulation of transporter activity negative regulation of molecular function negative regulation of potassium ion transmembrane transport regulation of potassium ion transmembrane transport regulation of molecular function 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 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 ubiquitin-dependent protein catabolic process behavior 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.