3V7D | pdb_00003v7d

Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	WD40 repeat-like	8043777	3001694	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	F-box domain	8043775	3000567	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	F-box domain	8043775	3000567	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	WD40 repeat-like	8043777	3001694	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Skp1 dimerisation domain-like	8043773	3000564	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Skp1 dimerisation domain-like	8043773	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)
D	WD40	e3v7dD3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: WD40	ECOD (v294.1)
B	WD40	e3v7dB3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: WD40	ECOD (v294.1)
C	MIR	e3v7dC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: MIR	ECOD (v294.1)
A	NAGLU_N	e3v7dA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: NAGLU_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
C	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
A	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
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
A, C	PF01466	Skp1 family, dimerisation domain (Skp1)	Skp1 family, dimerisation domain		Domain
A, C	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	Protein SIC1	enzyme regulator activity cyclin-dependent protein kinase regulator activity enzyme inhibitor activity protein kinase regulator activity protein kinase inhibitor activity molecular function inhibitor activity cyclin-dependent protein serine/threonine kinase inhibitor activity molecular function regulator activity cyclin-dependent protein serine/threonine kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity SCF ubiquitin ligase complex binding protein-containing complex binding enzyme regulator activity cyclin-dependent protein kinase regulator activity enzyme inhibitor activity protein kinase regulator activity protein kinase inhibitor activity molecular function inhibitor activity cyclin-dependent protein serine/threonine kinase inhibitor activity molecular function regulator activity cyclin-dependent protein serine/threonine kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity SCF ubiquitin ligase complex binding protein-containing complex binding binding	negative regulation of catabolic process regulation of biological process catabolic process regulation of cellular process macroautophagy negative regulation of metabolic process autophagy biological regulation negative regulation of biological process regulation of catabolic process regulation of autophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy negative regulation of cellular process negative regulation of catabolic process regulation of biological process catabolic process regulation of cellular process macroautophagy negative regulation of metabolic process autophagy biological regulation negative regulation of biological process regulation of catabolic process regulation of autophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy negative regulation of cellular process cellular process metabolic process process utilizing autophagic mechanism regulation of metabolic 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	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
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 snoRNA binding nucleic acid binding ubiquitin binding ubiquitin-like protein binding	ribonucleoprotein complex biogenesis 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 RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA cellular component organization or biogenesis RNA processing rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ribonucleoprotein complex biogenesis 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 RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA cellular component organization or biogenesis RNA processing rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process ribosomal small subunit biogenesis nucleic acid metabolic process biosynthetic 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 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 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein 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 intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membraneless 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
A, C	Suppressor of kinetochore protein 1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding 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 negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process translation gene expression macromolecule 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 chromosome organization membraneless organelle assembly kinetochore assembly kinetochore organization 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 heterochromatin organization 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 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 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process septin ring organization septin ring assembly septin cytoskeleton organization cytoskeleton organization subtelomeric heterochromatin formation 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 regulation of DNA-templated transcription G1/S transition of mitotic cell cycle cell cycle G1/S phase transition response to stimulus response to chemical cellular response to methylmercury response to methylmercury cellular response to stimulus 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 regulation of localization hexose transmembrane transport regulation of transport transport positive regulation of biological process carbohydrate transport establishment of localization positive regulation of D-glucose transmembrane transport transmembrane transport localization regulation of transmembrane transport positive regulation of transport D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport positive regulation of cellular process 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 intracellular monoatomic ion homeostasis	cellular anatomical structure endomembrane system protein-containing complex intracellular anatomical structure cytoplasm RAVE complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membraneless organelle chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region cellular anatomical structure endomembrane system protein-containing complex intracellular anatomical structure cytoplasm RAVE complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membraneless organelle chromosome CBF3 complex intracellular membrane-bounded organelle chromosomal region intracellular organelle organelle membraneless organelle chromosome, centromeric region 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR019775	WD40 repeat, conserved site	Conserved Site
B, D	IPR001810	F-box domain	Domain
B, D	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
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
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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.