2W99

Crystal Structure of CDK4 in complex with a D-type cyclin

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)
B	d2w99b_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	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)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8079139	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	Cyclin_C	e2w99A2	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_C	ECOD (1.6)
A	Cyclin_N	e2w99A1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_N	ECOD (1.6)
B	Pkinase_Tyr	e2w99B1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	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	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
A	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	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	G1/S-SPECIFIC CYCLIN-D1	histone deacetylase binding protein binding binding enzyme binding proline-rich region binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity histone deacetylase binding protein binding binding enzyme binding proline-rich region binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity protein kinase regulator activity kinase activator activity enzyme activator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase activator activity kinase regulator activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity kinase binding protein kinase binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus cell division regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling signaling negative regulation of biological process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus cell division regulation of cellular 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 cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling regulation of biological process negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition biological regulation 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 positive regulation of biological process positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle positive regulation of cellular process positive regulation of G1/S transition of mitotic cell cycle positive regulation of cell cycle positive regulation of cell cycle G1/S phase transition positive regulation of cell cycle phase transition response to light stimulus response to radiation response to abiotic stimulus response to UV response to UV-A multicellular organismal process regulation of developmental process positive regulation of cell population proliferation mammary gland development gland development positive regulation of mammary gland epithelial cell proliferation positive regulation of developmental process anatomical structure development regulation of multicellular organismal process epithelial cell proliferation developmental process epithelium development cell population proliferation positive regulation of epithelial cell proliferation animal organ development tissue development regulation of mammary gland epithelial cell proliferation mammary gland epithelium development regulation of cell population proliferation positive regulation of multicellular organismal process regulation of epithelial cell proliferation mammary gland epithelial cell proliferation fat cell differentiation cellular developmental process cell differentiation regulation of body fluid levels secretion transport establishment of localization body fluid secretion localization lactation regulation of biological quality re-entry into mitotic cell cycle RNA 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 transcription by RNA polymerase II 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 primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to hormone response to endogenous stimulus response to leptin cellular response to topologically incorrect protein endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein response to topologically incorrect protein response to endoplasmic reticulum stress regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation multicellular organism development negative regulation of cell differentiation regulation of multicellular organismal development negative regulation of epithelial cell differentiation negative regulation of developmental process animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration system development nervous system development generation of neurons neurogenesis neuron differentiation positive regulation of phosphorylation regulation of catalytic activity regulation of cyclin-dependent protein kinase activity regulation of transferase activity positive regulation of phosphate metabolic process positive regulation of metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cyclin-dependent protein kinase activity positive regulation of molecular function positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of phosphorylation neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of neuron apoptotic process cell surface receptor signaling pathway Wnt signaling pathway G2/M transition of mitotic cell cycle cell cycle G2/M phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition mammary gland lobule development mammary gland alveolus development	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 anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system 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 anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm cytosol cyclin D1-CDK4 complex cyclin D1-CDK6 complex centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction transcription regulator complex transcription repressor complex
B	CELL DIVISION PROTEIN KINASE 4	protein binding binding cyclin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding protein binding binding cyclin binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 cyclin-dependent protein kinase activity enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	response to stimulus response to chemical response to xenobiotic stimulus regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation regulation of type B pancreatic cell proliferation type B pancreatic cell proliferation biological regulation cellular process regulation of epithelial cell proliferation epithelial cell proliferation cell division response to stimulus response to chemical response to xenobiotic stimulus regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation regulation of type B pancreatic cell proliferation type B pancreatic cell proliferation biological regulation cellular process regulation of epithelial cell proliferation epithelial cell proliferation cell division response to interleukin-4 response to peptide response to cytokine cellular response to cytokine stimulus cellular response to interleukin-4 fibroblast proliferation positive regulation of cell population proliferation positive regulation of biological process regulation of fibroblast proliferation positive regulation of fibroblast proliferation positive regulation of cellular process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II regulation of DNA-templated transcription signaling signal transduction cell communication response to ketone response to alcohol response to phorbol 13-acetate 12-myristate cellular response to alcohol cellular response to phorbol 13-acetate 12-myristate cellular response to ketone protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus 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 cell cycle G2/M phase transition regulation of cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of cell cycle cellular response to ionomycin response to fatty acid cellular response to organic cyclic compound cellular response to ether cellular response to fatty acid response to ether response to ionomycin response to organic cyclic compound positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of cell cycle G2/M phase transition positive regulation of cell cycle positive regulation of cell cycle phase transition	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen 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 nuclear membrane membrane endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol transcription regulator complex nucleoplasm chromatin chromosome cyclin D2-CDK4 complex cyclin D1-CDK4 complex cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction cyclin D3-CDK4 complex

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P24385	plasma cell myeloma von Hippel-Lindau disease angiosarcoma transitional cell carcinoma breast cancer cancer leukemia breast carcinoma hyperparathyroidism squamous cell carcinoma nasopharyngeal carcinoma B-cell chronic lymphocytic leukemia esophageal squamous cell carcinoma mantle cell lymphoma malignant colon neoplasm plasma cell myeloma von Hippel-Lindau disease angiosarcoma transitional cell carcinoma breast cancer cancer leukemia breast carcinoma hyperparathyroidism squamous cell carcinoma nasopharyngeal carcinoma B-cell chronic lymphocytic leukemia esophageal squamous cell carcinoma mantle cell lymphoma malignant colon neoplasm hepatocellular carcinoma prostate cancer adenocarcinoma Mammary Neoplasms, Experimental salivary gland cancer kidney cancer adenoid cystic carcinoma squamous papilloma esophageal cancer thyroid adenoma granular cell carcinoma cecal neoplasm cervical cancer liver cancer melanoma brain cancer papilloma carcinoma cecum cancer hyperplasia salivary gland adenoid cystic carcinoma sarcomatoid carcinoma cutaneous melanoma thyroid gland carcinoma gastric cancer tubular adenocarcinoma hereditary diffuse gastric adenocarcinoma hydrolethalus syndrome psoriasis intestinal disease colorectal cancer medulloblastoma cribriform carcinoma schizophrenia liver disease myocardial ischemia cystic fibrosis lung benign neoplasm atypical teratoid rhabdoid tumor benign colon neoplasm oligodendroglioma eye disease major depressive disorder bone disease ovarian disease gastric neoplasm undifferentiated carcinoma malignant ependymoma pilocytic astrocytoma plasma cell neoplasm prostate disease intestinal polyp kidney neoplasm adenoma cribriform carcinoma of breast liver neoplasm endometrial cancer stomach disease lung cancer thyroid cancer lymphatic system disease osteosarcoma male breast carcinoma uterine disease malignant glioma pituitary cancer hematologic disease malignant mesothelioma breast disease precancerous condition primitive neuroectodermal tumor mammary neoplasms, animal colonic neoplasm coronary artery disease large cell medulloblastoma myeloid neoplasm astrocytic tumor neoplasm of esophagus endometrial carcinoma subependymal giant cell astrocytoma lung disease benign urinary system neoplasm ovarian cancer brain disease papillomatosis glioblastoma
B	Pharos: P11802	melanoma, cutaneous malignant, susceptibility to, 3 familial melanoma liposarcoma well-differentiated liposarcoma Mammary Neoplasms, Experimental carcinoma melanoma gastric cancer sarcomatoid carcinoma cutaneous melanoma pleomorphic liposarcoma cancer Dedifferentiated liposarcoma ovarian cancer glioblastoma melanoma, cutaneous malignant, susceptibility to, 3 familial melanoma liposarcoma well-differentiated liposarcoma Mammary Neoplasms, Experimental carcinoma melanoma gastric cancer sarcomatoid carcinoma cutaneous melanoma pleomorphic liposarcoma cancer Dedifferentiated liposarcoma ovarian cancer glioblastoma hereditary diffuse gastric adenocarcinoma acute myeloid leukemia large cell medulloblastoma astrocytic tumor lung adenocarcinoma lymphoma malignant glioma brainstem cancer connective tissue disease nasopharyngeal carcinoma non-small cell lung carcinoma pilocytic astrocytoma hematologic disease atypical lipomatous tumor lung cancer malignant colon neoplasm brain cancer malignant mesothelioma breast disease eye disease oligodendroglioma gastric neoplasm hepatocellular carcinoma primitive neuroectodermal tumor undifferentiated carcinoma atypical teratoid rhabdoid tumor lung disease malignant ependymoma mammary neoplasms, animal medulloblastoma

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.