1W98

The structural basis of CDK2 activation by cyclin E

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1w98a2	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Cyclin-dependent PK, CDK2	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1w98a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1w98b1	All alpha proteins	Cyclin-like	Cyclin-like	Cyclin	G1/S-specific cyclin-E1	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)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8040310	3000066	SCOP2B (2022-06-29)
B	SCOP2 Family	Cyclin	8020056	4001102	SCOP2 (2022-06-29)
B	SCOP2 Family	Cyclin	8020057	4001102	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cyclin-like	8032436	3000768	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cyclin-like	8032437	3000768	SCOP2 (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	e1w98A1	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	Cyclin_C	e1w98B1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_C	ECOD (1.6)
B	Cyclin_N	e1w98B2	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_N	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)
B	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain
B	PF00134	Cyclin, N-terminal domain (Cyclin_N)	Cyclin, N-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.	Domain
B	PF02984	Cyclin, C-terminal domain (Cyclin_C)	Cyclin, C-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the C-terminal domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CELL DIVISION PROTEIN 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 cellular biosynthetic process cellular metabolic process biological regulation 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 positive regulation of nucleobase-containing compound metabolic process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process DNA replication positive regulation of DNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound 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 non-membrane-bounded 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 cellular metabolic process 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 cellular biosynthetic 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 cellular process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular 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 chromatin organization regulation of heterochromatin formation regulation of chromatin organization regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization negative regulation of gene expression negative regulation of gene expression, epigenetic regulation of cellular component organization positive regulation of cellular component organization positive regulation of heterochromatin formation positive regulation of chromatin organization chromatin remodeling heterochromatin formation positive regulation of cellular component biogenesis epigenetic regulation of gene expression regulation of cellular component biogenesis	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 intracellular anatomical structure organelle nuclear envelope nucleus 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 intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol transcription regulator complex sex chromosome intracellular non-membrane-bounded organelle chromosome non-membrane-bounded organelle 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	G1/S-SPECIFIC CYCLIN E1	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding binding kinase binding enzyme binding protein kinase binding enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process cell division meiotic chromosome segregation sexual reproduction reproductive process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process cell division meiotic chromosome segregation sexual reproduction reproductive process meiotic cell cycle organelle fission chromosome organization meiotic cell cycle process cellular component organization chromosome organization involved in meiotic cell cycle nuclear division organelle organization meiosis I meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation meiotic nuclear division homologous chromosome segregation cell cycle cellular component organization or biogenesis chromosome segregation cell cycle process regulation of cell cycle phase transition regulation of cellular process positive regulation of biological process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle regulation of cell cycle positive regulation of cellular process positive regulation of G1/S transition of mitotic cell cycle regulation of biological process regulation of cell cycle process biological regulation positive regulation of cell cycle regulation of mitotic cell cycle phase transition positive regulation of cell cycle G1/S phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle positive regulation of cell cycle phase transition G1/S transition of mitotic cell cycle mitotic cell cycle phase transition telomere organization telomere maintenance mesenchymal stem cell proliferation regulation of stem cell proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of mesenchymal stem cell proliferation regulation of mesenchymal stem cell proliferation positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation protein phosphorylation phosphorylation cellular metabolic process macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process protein localization regulation of localization cellular localization regulation of protein localization localization regulation of cellular localization cellular macromolecule localization macromolecule localization cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction Wnt signaling pathway 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 DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II 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 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 regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic 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 regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process	intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin E1-CDK2 complex cyclin-dependent protein kinase holoenzyme complex transferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000719	Protein kinase domain	Domain
A	IPR050108	Cyclin-dependent kinase	Family
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B	IPR048258	Cyclins, cyclin-box	Conserved Site
B	IPR004367	Cyclin, C-terminal domain	Domain
B	IPR006671	Cyclin, N-terminal	Domain
B	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B	IPR039361	Cyclin	Family
B	IPR013763	Cyclin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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	Pharos: P24864	urinary bladder cancer breast carcinoma medulloblastoma ovarian cancer medullomyoblastoma with myogenic differentiation adult medulloblastoma cancer melanotic medulloblastoma breast cancer childhood medulloblastoma Neoplasm of uncertain or unknown behavior of ovary pancreatic intraductal papillary-mucinous neoplasm adrenal cortex carcinoma desmoplastic/nodular medulloblastoma hepatocellular carcinoma urinary bladder cancer breast carcinoma medulloblastoma ovarian cancer medullomyoblastoma with myogenic differentiation adult medulloblastoma cancer melanotic medulloblastoma breast cancer childhood medulloblastoma Neoplasm of uncertain or unknown behavior of ovary pancreatic intraductal papillary-mucinous neoplasm adrenal cortex carcinoma desmoplastic/nodular medulloblastoma hepatocellular carcinoma lung cancer non-small cell lung carcinoma ovarian carcinoma psoriasis urinary bladder neoplasm osteosarcoma ovarian neoplasm lung adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.