6XK9

Cereblon in complex with DDB1, CC-90009, and GSPT1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth Y]	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
B [auth Y]	SCOP2B Superfamily	WD40 repeat-like	8052531	3001694	SCOP2B (2022-06-29)
B [auth Y]	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
B [auth Y]	SCOP2B Superfamily	WD40 repeat-like	8051194	3001694	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	WD40 repeat-like	8051194	3001694	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	WD40 repeat-like	8052531	3001694	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth X]	GTP_EFTU_D2_1	e6xk9X2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
A [auth X]	GTP_EFTU_D3_1	e6xk9X1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
D [auth A]	GTP_EFTU_D2_1	e6xk9A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
D [auth A]	GTP_EFTU_D3_1	e6xk9A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
B [auth Y]	CPSF_A_N	e6xk9Y1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: CPSF_A_N	ECOD (1.6)
B [auth Y]	MMS1_N_C	e6xk9Y2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N_C	ECOD (1.6)
B [auth Y]	MMS1_N_N	e6xk9Y3	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N_N	ECOD (1.6)
B [auth Y]	CPSF_A_C	e6xk9Y4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: CPSF_A_C	ECOD (1.6)
E [auth B]	CPSF_A_N	e6xk9B1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: CPSF_A_N	ECOD (1.6)
E [auth B]	MMS1_N_C	e6xk9B4	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N_C	ECOD (1.6)
E [auth B]	MMS1_N_N	e6xk9B3	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N_N	ECOD (1.6)
E [auth B]	CPSF_A_C	e6xk9B2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: CPSF_A_C	ECOD (1.6)
C [auth Z]	LON_substr_bdg	e6xk9Z1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: LON_substr_bdg	ECOD (1.6)
C [auth Z]	Yippee-Mis18_1	e6xk9Z2	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 C]	LON_substr_bdg	e6xk9C2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: LON_substr_bdg	ECOD (1.6)
F [auth C]	Yippee-Mis18_1	e6xk9C1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: Yippee-Mis18_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth X], D [auth A]	PF22594	GTP-eEF1A C-terminal domain-like (GTP-eEF1A_C)	GTP-eEF1A C-terminal domain-like	This entry represents a beta-barrel domain that is found C-terminal in homologues of elongation factor eEF1A.	Domain
A [auth X], D [auth A]	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
B [auth Y], E [auth B]	PF10433	Mono-functional DNA-alkylating methyl methanesulfonate N-term (MMS1_N)	Mono-functional DNA-alkylating methyl methanesulfonate N-term	-	Repeat
B [auth Y], E [auth B]	PF03178	CPSF A subunit region (CPSF_A)	CPSF A subunit region	-	Repeat
C [auth Z], F [auth C]	PF02190	ATP-dependent protease La (LON) substrate-binding domain (LON_substr_bdg)	ATP-dependent protease La (LON) substrate-binding domain	-	Family
C [auth Z], F [auth C]	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 [auth X], D [auth A]	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation release factor activity nucleic acid binding translation termination factor activity translation factor activity, RNA binding RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation release factor activity nucleic acid binding translation termination factor activity translation factor activity, RNA binding RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	mitotic cell cycle process cellular process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process protein alkylation methylation protein methylation macromolecule modification metabolic process mitotic cell cycle process cellular process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process protein alkylation methylation protein methylation macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process macromolecule methylation cellular component disassembly protein-containing complex organization cellular biosynthetic process cellular metabolic process protein-containing complex disassembly translation gene expression macromolecule biosynthetic process cellular component organization biosynthetic process translational termination cellular component organization or biogenesis regulation of cellular process regulation of cellular component organization regulation of protein-containing complex disassembly regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of biosynthetic process regulation of biological process regulation of protein metabolic process regulation of translational termination biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process	intracellular organelle intracellular anatomical structure cytosolic ribosome organelle intracellular non-membrane-bounded organelle ribosome cytoplasm cellular anatomical entity cytosol non-membrane-bounded organelle protein-containing complex translation release factor complex
B [auth Y], E [auth B]	DNA damage-binding protein 1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding protein binding cullin family protein binding damaged DNA binding WD40-repeat domain binding protein domain specific binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process proteolysis proteasomal protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process proteolysis proteasomal protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process apoptotic process cell death programmed cell death protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of biological process negative regulation of reproductive process regulation of reproductive process reproductive process biological regulation negative regulation of biological process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of cellular process epigenetic programming in the zygotic pronuclei cellular biosynthetic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis regulation of biosynthetic process epigenetic programming of gene expression epigenetic regulation of gene expression cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle mitotic cell cycle phase transition cell cycle process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair positive regulation of viral genome replication positive regulation of viral process positive regulation of biological process viral life cycle regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication developmental process cellular developmental process cell development developmental process involved in reproduction programmed cell death involved in cell development cell differentiation anatomical structure development ectopic germ cell programmed cell death nucleotide-excision repair response to light stimulus cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation response to UV UV-damage excision repair response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV monosaccharide metabolic process positive regulation of cellular metabolic process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process positive regulation of cellular biosynthetic process glucose metabolic process rhythmic process circadian rhythm regulation of circadian rhythm negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process positive regulation of protein metabolic process regulation of protein metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process positive regulation of macromolecule metabolic process regulation of protein catabolic process biological process involved in interspecies interaction between organisms biological process involved in interaction with symbiont biological process involved in symbiotic interaction regulation by virus of viral protein levels in host cell positive regulation by virus of viral protein levels in host cell regulation of biological quality proteasome-mediated ubiquitin-dependent protein catabolic process regulation of developmental process negative regulation of developmental process exit from host cell viral release from host cell biological process involved in interaction with host meiotic chromosome segregation sexual reproduction non-membrane-bounded organelle assembly microtubule cytoskeleton organization female gamete generation meiotic cell cycle process gamete generation cellular component biogenesis cellular component assembly female meiotic nuclear division meiotic nuclear division chromosome segregation spindle organization organelle assembly organelle fission meiotic cell cycle multicellular organismal reproductive process meiotic spindle organization meiotic spindle assembly spindle assembly nuclear division organelle organization nuclear chromosome segregation microtubule-based process cytoskeleton organization spindle assembly involved in female meiosis cell surface receptor signaling pathway signaling cell communication signal transduction Wnt signaling pathway	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle intracellular non-membrane-bounded organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region chromosomal region non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen 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 nucleoplasm site of double-strand break site of DNA damage Cul4B-RING E3 ubiquitin ligase complex
C [auth Z], F [auth C]	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 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 protein ubiquitination macromolecule modification metabolic process primary 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	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol perinuclear region of 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 cellular anatomical entity intracellular anatomical structure cytoplasm cytosol perinuclear region of 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 [auth X], D [auth A]	IPR050100	Translation factor GTPase superfamily members	Family
A [auth X], D [auth A]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A [auth X], D [auth A]	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A [auth X], D [auth A]	IPR031157	Tr-type G domain, conserved site	Conserved Site
A [auth X], D [auth A]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A [auth X], D [auth A]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A [auth X], D [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth Y], E [auth B]	IPR018846	Cleavage/polyadenylation specificity factor, A subunit, N-terminal	Domain
B [auth Y], E [auth B]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B [auth Y], E [auth B]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B [auth Y], E [auth B]	IPR004871	Cleavage/polyadenylation specificity factor, A subunit, C-terminal	Domain
B [auth Y], E [auth B]	IPR050358	RSE1/DDB1/CFT1/CPSF1	Family
C [auth Z], F [auth C]	IPR015947	PUA-like superfamily	Homologous Superfamily
C [auth Z], F [auth C]	IPR046336	Lon protease, N-terminal domain superfamily	Homologous Superfamily
C [auth Z], F [auth C]	IPR004910	Yippee/Mis18/Cereblon	Domain
C [auth Z], F [auth C]	IPR003111	Lon protease, N-terminal domain	Domain
C [auth Z], F [auth C]	IPR034750	CULT domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth X], D [auth A]	Pharos: P15170	pancreatic ductal adenocarcinoma Pick disease psoriasis tuberculosis adenoma cystic fibrosis glioblastoma large cell medulloblastoma malignant ependymoma myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma Sjogren syndrome astrocytic tumor pancreatic ductal adenocarcinoma Pick disease psoriasis tuberculosis adenoma cystic fibrosis glioblastoma large cell medulloblastoma malignant ependymoma myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma Sjogren syndrome astrocytic tumor ductal breast carcinoma in situ hereditary spastic paraplegia lung adenocarcinoma malignant glioma non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive supranuclear palsy testicular germ cell tumor breast carcinoma gastric carcinoma invasive ductal breast carcinoma lung cancer medulloblastoma oligodendroglioma
B [auth Y], E [auth B]	Pharos: Q16531	Disease Exacerbation gastric cancer lung cancer xeroderma pigmentosum gastric neoplasm drug-induced liver injury hereditary diffuse gastric adenocarcinoma psoriasis
C [auth Z], F [auth C]	Pharos: Q96SW2	intellectual disability, autosomal recessive 2 plasma cell myeloma 3p- syndrome intellectual disability toxic or drug-related embryofetopathy central nervous system malformation Erythema nodosum leprosum mantle cell lymphoma non-small cell lung carcinoma follicular lymphoma large cell medulloblastoma marginal zone lymphoma osteosarcoma POEMS syndrome attention deficit hyperactivity disorder, inattentive type intellectual disability, autosomal recessive 2 plasma cell myeloma 3p- syndrome intellectual disability toxic or drug-related embryofetopathy central nervous system malformation Erythema nodosum leprosum mantle cell lymphoma non-small cell lung carcinoma follicular lymphoma large cell medulloblastoma marginal zone lymphoma osteosarcoma POEMS syndrome attention deficit hyperactivity disorder, inattentive type lung adenocarcinoma myelodysplastic syndrome ovarian cancer

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.