4I6J

A ubiquitin ligase-substrate complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4i6ja1	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4i6jc2	All alpha proteins	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4i6jc1	Alpha and beta proteins (a+b)	POZ domain	POZ domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Skp1 dimerisation domain-like	8038683	3000564	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	FAD_binding_7	e4i6jA3	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
A	DNA_photolyase	e4i6jA4	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
B	LRR_8_4	e4i6jB3	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_4	ECOD (1.6)
B	F-box-like	e4i6jB2	A: alpha arrays	X: F-box domain (From Topology)	H: F-box domain (From Topology)	T: F-box domain	F: F-box-like	ECOD (1.6)
C	Skp1_POZ	e4i6jC1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: Skp1_POZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
B	1.20.1280.50	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
B	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
C	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00875	DNA photolyase (DNA_photolyase)	DNA photolyase	This domain binds a light harvesting cofactor.	Domain
A	PF03441	FAD binding domain of DNA photolyase (FAD_binding_7)	FAD binding domain of DNA photolyase	-	Domain
B	PF12937	F-box-like (F-box-like)	F-box-like	This is an F-box-like family.	Domain
C	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Cryptochrome-2	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding damaged DNA binding protein binding kinase binding enzyme binding protein kinase binding phosphatase binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding molecular transducer activity photoreceptor activity signaling receptor activity single-stranded DNA binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process multicellular organismal process regulation of localization system process regulation of system process negative regulation of transport negative regulation of lipid localization cell communication regulation of glucocorticoid secretion localization regulation of steroid hormone secretion negative regulation of secretion negative regulation of hormone secretion negative regulation of secretion by cell regulation of biological quality negative regulation of steroid hormone secretion regulation of hormone levels lipid transport regulation of corticosteroid hormone secretion establishment of localization regulation of secretion endocrine hormone secretion lipid export from cell negative regulation of corticosteroid hormone secretion glucocorticoid secretion negative regulation of multicellular organismal process regulation of endocrine process corticosteroid hormone secretion regulation of hormone secretion transport signaling negative regulation of signaling steroid hormone secretion regulation of lipid transport hormone secretion negative regulation of cell communication secretion by cell regulation of secretion by cell signal release regulation of multicellular organismal process negative regulation of glucocorticoid secretion regulation of signaling negative regulation of lipid transport secretion regulation of transport lipid localization export from cell cell-cell signaling endocrine process regulation of lipid localization macromolecule localization hormone transport regulation of cell communication rhythmic process circadian rhythm regulation of circadian rhythm response to stimulus response to activity response to light stimulus response to radiation response to abiotic stimulus sodium-dependent phosphate transport regulation of phosphate transport regulation of sodium-dependent phosphate transport phosphate ion transport inorganic anion transport protein localization establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport nuclear transport intracellular transport protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport cellular macromolecule localization protein localization to organelle establishment of localization in cell protein import into nucleus intracellular protein transport negative regulation of circadian rhythm circadian regulation of gene expression entrainment of circadian clock response to external stimulus photoperiodism entrainment of circadian clock by photoperiod response to hormone response to chemical response to endogenous stimulus response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound cellular response to stimulus intracellular receptor signaling pathway response to lipid negative regulation of intracellular signal transduction regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction cellular response to endogenous stimulus negative regulation of intracellular steroid hormone receptor signaling pathway regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound steroid hormone receptor signaling pathway cellular response to hormone stimulus negative regulation of response to stimulus cellular response to organic cyclic compound nuclear receptor-mediated corticosteroid signaling pathway negative regulation of signal transduction negative regulation of glucocorticoid receptor signaling pathway regulation of glucocorticoid receptor signaling pathway cellular response to chemical stimulus regulation of response to stimulus cellular response to lipid nuclear receptor-mediated signaling pathway nuclear receptor-mediated glucocorticoid signaling pathway lipid storage maintenance of location transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex Cry-Per complex transcription repressor complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex Cry-Per complex transcription repressor complex membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear lumen cytosol extracellular region
B	F-box/LRR-repeat protein 3	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity	rhythmic process response to light stimulus regulation of biological process entrainment of circadian clock response to stimulus circadian rhythm biological regulation response to external stimulus regulation of circadian rhythm photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod protein destabilization rhythmic process response to light stimulus regulation of biological process entrainment of circadian clock response to stimulus circadian rhythm biological regulation response to external stimulus regulation of circadian rhythm photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod protein destabilization regulation of protein stability regulation of biological quality 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 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex
C	S-phase kinase-associated protein 1	ubiquitin ligase complex scaffold activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein domain specific binding cullin family protein binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity molecular function activator activity molecular function regulator activity beta-catenin binding F-box domain binding	maintenance of protein location protein localization cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle maintenance of protein location protein localization cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell cellular macromolecule localization macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle 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 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein modification process regulation of catalytic activity positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination regulation of transferase activity positive regulation of post-translational protein modification regulation of primary metabolic process regulation of ubiquitin protein ligase activity positive regulation of metabolic process positive regulation of molecular function positive regulation of ubiquitin protein ligase activity positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of ubiquitin-protein transferase activity regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process positive regulation of transferase activity regulation of post-translational protein modification regulation of protein metabolic process biological regulation positive regulation of catalytic activity regulation of macromolecule metabolic process positive regulation of ubiquitin-protein transferase activity regulation of molecular function regulation of metabolic process protein polyubiquitination protein K48-linked ubiquitination protein monoubiquitination cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity PcG protein complex centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul7-RING ubiquitin ligase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR036155	Cryptochrome/photolyase, N-terminal domain superfamily	Homologous Superfamily
A	IPR002081	Cryptochrome/DNA photolyase class 1	Family
A	IPR036134	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Homologous Superfamily
A	IPR006050	DNA photolyase, N-terminal	Domain
A	IPR005101	Cryptochrome/DNA photolyase, FAD-binding domain	Domain
B	IPR036047	F-box-like domain superfamily	Homologous Superfamily
B	IPR001810	F-box domain	Domain
B	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C	IPR016073	SKP1 component, POZ domain	Domain
C	IPR001232	S-phase kinase-associated protein 1-like	Family
C	IPR036296	SKP1-like, dimerisation domain superfamily	Homologous Superfamily
C	IPR016072	SKP1 component, dimerisation	Domain
C	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
C	IPR016897	S-phase kinase-associated protein 1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q9UKT7	astrocytic tumor glioblastoma neuronal ceroid lipofuscinosis 5 ovarian cancer spina bifida atypical teratoid rhabdoid tumor large cell medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma ulcerative colitis bipolar disorder malignant ependymoma osteosarcoma primitive neuroectodermal tumor
C	Pharos: P63208	allergic rhinitis esophageal adenocarcinoma hypothyroidism medulloblastoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer plasma cell myeloma systemic lupus erythematosus breast cancer Hashimoto thyroiditis malignant glioma allergic rhinitis esophageal adenocarcinoma hypothyroidism medulloblastoma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma ovarian cancer plasma cell myeloma systemic lupus erythematosus breast cancer Hashimoto thyroiditis malignant glioma pancreatic ductal adenocarcinoma rheumatoid arthritis

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.