3MKS

Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3mksa2	All alpha proteins	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3mksa1	Alpha and beta proteins (a+b)	POZ domain	POZ domain	BTB/POZ domain	Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d3mksc2	All alpha proteins	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Skp1 dimerisation domain-like	Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d3mksc1	Alpha and beta proteins (a+b)	POZ domain	POZ domain	BTB/POZ domain	Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3mksb1	All alpha proteins	F-box domain	F-box domain	F-box domain	Cdc4 F-box and linker domains	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3mksb2	All beta proteins	7-bladed beta-propeller	WD40 repeat-like	WD40-repeat	Cdc4 propeller domain	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d3mksd1	All alpha proteins	F-box domain	F-box domain	F-box domain	Cdc4 F-box and linker domains	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d3mksd2	All beta proteins	7-bladed beta-propeller	WD40 repeat-like	WD40-repeat	Cdc4 propeller domain	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Skp1 dimerisation domain-like	8043773	3000564	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Skp1 dimerisation domain-like	8043773	3000564	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	WD40 repeat-like	8043777	3001694	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	F-box domain	8043775	3000567	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	F-box domain	8043775	3000567	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	WD40 repeat-like	8043777	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	Skp1_POZ	e3mksA1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: Skp1_POZ	ECOD (1.6)
C	Skp1_POZ	e3mksC1	A: a+b two layers	X: POZ domain (From Topology)	H: POZ domain (From Topology)	T: POZ domain	F: Skp1_POZ	ECOD (1.6)
B	ANAPC4_WD40_8	e3mksB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: ANAPC4_WD40_8	ECOD (1.6)
B	F-box-like	e3mksB2	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)
D	ANAPC4_WD40_8	e3mksD3	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: ANAPC4_WD40_8	ECOD (1.6)
D	F-box-like	e3mksD4	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
C	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
B	1.20.1280.50	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
D	1.20.1280.50	Mainly Alpha	Up-down Bundle	Monooxygenase		CATH (4.3.0)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain	-	Domain
B, D	PF00646	F-box domain (F-box)	F-box domain	This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07 ...	This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07723) and the WD repeat (Pfam:PF00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression [1-2].	Domain
B, D	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B, D	PF16856	Cell division control protein 4 dimerisation domain (CDC4_D)	Cell division control protein 4 dimerisation domain	This is the dimerisation domain (D domain) of fungal cell division control protein 4 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Suppressor of kinetochore protein 1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding DNA replication origin binding protein binding cullin family protein binding	regulation of biological process regulation of cellular process regulation of cellular component organization protein-containing complex organization biological regulation regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis cell cycle regulation of biological process regulation of cellular process regulation of cellular component organization protein-containing complex organization biological regulation regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis cell cycle mitotic cell cycle cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process translation gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of cytoplasmic translation negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process cytoplasmic translation metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of cytoplasmic translation regulation of metabolic process regulation of mitotic cell cycle regulation of cell cycle organelle fusion organelle organization mitochondrial fusion mitochondrion organization proton-transporting V-type ATPase complex assembly vacuolar proton-transporting V-type ATPase complex assembly proton-transporting two-sector ATPase complex assembly organelle assembly non-membrane-bounded organelle assembly chromosome organization protein-DNA complex assembly protein-DNA complex organization kinetochore assembly kinetochore organization centromere complex assembly regulation of cell cycle phase transition cell cycle phase transition exit from mitosis cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission regulation of mitotic cell cycle phase transition nuclear division mitotic cell cycle process regulation of exit from mitosis mitotic cell cycle phase transition chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression constitutive heterochromatin formation silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic macromolecule modification post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal protein ubiquitination organonitrogen compound catabolic process 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 organic substance catabolic process septin ring organization septin ring assembly septin cytoskeleton organization cytoskeleton organization oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process organic acid metabolic process regulation of sulfur metabolic process regulation of small molecule metabolic process sulfur compound metabolic process small molecule metabolic process regulation of sulfur amino acid metabolic process regulation of localization hexose transmembrane transport transport positive regulation of biological process carbohydrate transport localization positive regulation of transmembrane transport glucose transmembrane transport positive regulation of cellular process positive regulation of glucose transmembrane transport regulation of transport organic substance transport establishment of localization transmembrane transport regulation of glucose transmembrane transport regulation of transmembrane transport positive regulation of transport monosaccharide transmembrane transport carbohydrate transmembrane transport subtelomeric heterochromatin formation telomere organization RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by galactose regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription G1/S transition of mitotic cell cycle cell cycle G1/S phase transition cellular response to stimulus response to organic substance cellular response to chemical stimulus response to stimulus response to chemical cellular response to methylmercury response to methylmercury cellular response to organic substance DNA damage checkpoint signaling signaling negative regulation of cell cycle intracellular signal transduction negative regulation of mitotic cell cycle cell communication mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition signal transduction mitotic intra-S DNA damage checkpoint signaling DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage cell cycle G2/M phase transition G2/M transition of mitotic cell cycle homeostatic process intracellular pH reduction regulation of intracellular pH vacuolar acidification cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis regulation of biological quality monoatomic cation homeostasis regulation of cellular pH intracellular monoatomic ion homeostasis	cellular anatomical entity endomembrane system protein-containing complex intracellular anatomical structure cytoplasm RAVE complex membrane-bounded organelle nucleus nuclear protein-containing complex chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region intracellular organelle cellular anatomical entity endomembrane system protein-containing complex intracellular anatomical structure cytoplasm RAVE complex membrane-bounded organelle nucleus nuclear protein-containing complex chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region intracellular organelle organelle intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome chromosome, telomeric region
B, D	Cell division control protein 4	phosphoprotein binding protein binding binding phosphoserine residue binding protein phosphorylated amino acid binding RNA binding U3 snoRNA binding organic cyclic compound binding snoRNA binding nucleic acid binding ubiquitin binding ubiquitin-like protein binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis nucleobase-containing compound metabolic process ribosome biogenesis organic substance metabolic process maturation of SSU-rRNA organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis nucleobase-containing compound metabolic process ribosome biogenesis organic substance metabolic process maturation of SSU-rRNA organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process ribosomal small subunit biogenesis nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process nucleic acid catabolic process cellular process metabolic process macromolecule metabolic process endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cell division sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation organonitrogen compound metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal organonitrogen compound catabolic process 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 organic substance catabolic process mitotic cell cycle 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 sexual reproduction reproductive process meiotic cell cycle cell cycle G2/M phase transition G2/M transition of mitotic cell cycle rRNA 5'-end processing endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) RNA 5'-end processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix nucleolus intracellular non-membrane-bounded organelle non-membrane-bounded organelle cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex nuclear SCF ubiquitin ligase complex nuclear protein-containing complex nuclear ubiquitin ligase complex 90S preribosome preribosome ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR016073	SKP1 component, POZ domain	Domain
A, C	IPR001232	S-phase kinase-associated protein 1-like	Family
A, C	IPR036296	SKP1-like, dimerisation domain superfamily	Homologous Superfamily
A, C	IPR016072	SKP1 component, dimerisation	Domain
A, C	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A, C	IPR016897	S-phase kinase-associated protein 1	Family
B, D	IPR019775	WD40 repeat, conserved site	Conserved Site
B, D	IPR001810	F-box domain	Domain
B, D	IPR031740	Cell division control protein 4, dimerisation domain	Domain
B, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B, D	IPR036047	F-box-like domain superfamily	Homologous Superfamily
B, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B, D	IPR001680	WD40 repeat	Repeat
B, D	IPR020472	G-protein beta WD-40 repeat	Repeat

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.