5UQ1

Crystal structure of human Cdk2-Spy1 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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8040310	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8040310	3000066	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	Pkinase_Tyr	e5uq1A1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
C	Pkinase_Tyr	e5uq1C1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
B	UNK_F_TYPE	e5uq1B1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: UNK_F_TYPE	ECOD (1.6)
D	UNK_F_TYPE	e5uq1D1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain
B, D	PF11357	Cell cycle regulatory protein (Spy1)	Cell cycle regulatory protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Cyclin-dependent kinase 2	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity cyclin-dependent protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein binding protein domain specific binding cyclin binding protein serine kinase activity cation binding magnesium ion binding metal ion binding	cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organelle organization cellular response to stress DNA damage response response to stress cellular response to stimulus telomere maintenance in response to DNA damage response to stimulus telomere organization chromosome organization primary metabolic process DNA metabolic process nucleic acid metabolic process telomere maintenance cellular component organization nucleobase-containing compound metabolic process organelle organization cellular response to stress DNA damage response response to stress cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process cell division microtubule organizing center organization microtubule cytoskeleton organization centrosome duplication centrosome cycle microtubule-based process cell cycle cytoskeleton organization cell cycle process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process DNA replication positive regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of cell cycle phase transition DNA damage checkpoint signaling signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction regulation of cell cycle negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition cellular senescence centriole assembly organelle assembly membraneless organelle assembly cellular component biogenesis cellular component assembly centriole replication macromolecule modification protein metabolic process post-translational protein modification protein modification process protein phosphorylation phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process DNA repair cell cycle G2/M phase transition regulation of G2/M transition of mitotic cell cycle G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification negative regulation of RNA biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to nitric oxide cellular response to chemical stimulus response to chemical response to nitric oxide cellular response to reactive nitrogen species regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation regulation of DNA-templated DNA replication positive regulation of DNA-templated DNA replication positive regulation of DNA-templated DNA replication initiation small GTPase-mediated signal transduction Ras protein signal transduction intracellular signaling cassette localization transport monoatomic ion transport potassium ion transport monoatomic cation transport establishment of localization metal ion transport cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process catabolic process regulation of anaphase-promoting complex-dependent catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process anaphase-promoting complex-dependent catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process sexual reproduction reproductive process meiotic cell cycle positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of heterochromatin formation chromatin organization positive regulation of chromatin organization chromatin remodeling regulation of heterochromatin formation regulation of chromatin organization heterochromatin formation positive regulation of cellular component biogenesis epigenetic regulation of gene expression regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization positive regulation of chromosome organization negative regulation of gene expression negative regulation of gene expression, epigenetic	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol transcription regulator complex sex chromosome membraneless organelle intracellular membraneless organelle chromosome X chromosome Cajal body membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen Y chromosome cyclin E2-CDK2 complex male germ cell nucleus germ cell nucleus chromosome, telomeric region chromosomal region cyclin A2-CDK2 complex condensed chromosome centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton cyclin E1-CDK2 complex endosome intracellular vesicle cytoplasmic vesicle vesicle cyclin A1-CDK2 complex
B, D	Speedy protein A	protein binding binding kinase binding enzyme binding protein kinase binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process establishment of protein localization to telomere protein localization establishment of protein localization cellular localization protein localization to chromosome, telomeric region establishment of localization localization establishment of protein localization to organelle protein localization to chromosome cellular macromolecule localization macromolecule localization protein localization to organelle establishment of protein localization to chromosome developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular developmental process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation cell differentiation anatomical structure development germ cell development 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 regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process establishment of organelle localization meiotic chromosome segregation meiotic attachment of telomere to nuclear envelope meiotic cell cycle process cellular component organization telomere localization meiosis I chromosome localization organelle localization establishment of localization in cell meiotic nuclear division cellular component organization or biogenesis chromosome segregation meiotic cell cycle organelle fission meiotic telomere clustering meiotic telomere tethering at nuclear periphery chromosome organization chromosome organization involved in meiotic cell cycle nuclear division organelle organization chromosome localization to nuclear envelope involved in homologous chromosome segregation telomere tethering at nuclear periphery meiosis I cell cycle process nuclear chromosome segregation chromosome attachment to the nuclear envelope homologous chromosome segregation establishment of chromosome localization telomere organization DNA metabolic process nucleic acid metabolic process telomere maintenance nucleobase-containing compound metabolic process telomere capping male meiotic nuclear division regulation of cyclin-dependent protein kinase activity positive regulation of protein serine/threonine kinase activity positive regulation of cyclin-dependent protein serine/threonine kinase activity regulation of cyclin-dependent protein serine/threonine kinase activity regulation of protein serine/threonine kinase activity positive regulation of cyclin-dependent protein kinase activity regulation of cell cycle positive regulation of cell cycle	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system XY body sex chromosome membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system XY body sex chromosome membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR000719	Protein kinase domain	Domain
A, C	IPR050108	Cyclin-dependent kinase	Family
A, C	IPR017441	Protein kinase, ATP binding site	Binding Site
A, C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, C	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B, D	IPR052316	Speedy/Ringo cell cycle regulator	Family
B, D	IPR020984	Cell cycle regulatory protein Speedy	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P24941	melanoma glioblastoma large cell medulloblastoma malignant glioma medulloblastoma osteosarcoma adrenal cortex carcinoma primitive neuroectodermal tumor alopecia areata vitiligo atypical teratoid rhabdoid tumor Childhood Diffuse Large B-Cell Lymphoma diffuse large B-cell lymphoma malignant colon neoplasm pilocytic astrocytoma melanoma glioblastoma large cell medulloblastoma malignant glioma medulloblastoma osteosarcoma adrenal cortex carcinoma primitive neuroectodermal tumor alopecia areata vitiligo atypical teratoid rhabdoid tumor Childhood Diffuse Large B-Cell Lymphoma diffuse large B-cell lymphoma malignant colon neoplasm pilocytic astrocytoma psoriasis asthma breast disease cleft lip eye disease Hashimoto thyroiditis hypothyroidism malignant ependymoma malignant mesothelioma polycystic ovary syndrome allergic rhinitis rheumatoid arthritis attention deficit hyperactivity disorder, inattentive type cancer cutaneous melanoma gastroesophageal reflux disease hematologic disease
B, D	Pharos: Q5MJ70	breast carcinoma estrogen-receptor negative breast 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.