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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9D0W

Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4

This is a non-PDB format compatible entry.
Functional Information from GO Data
ChainGOidnamespacecontents
A0000109cellular_componentnucleotide-excision repair complex
A0000781cellular_componentchromosome, telomeric region
A0003676molecular_functionnucleic acid binding
A0003677molecular_functionDNA binding
A0003684molecular_functiondamaged DNA binding
A0005515molecular_functionprotein binding
A0005576cellular_componentextracellular region
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005730cellular_componentnucleolus
A0005737cellular_componentcytoplasm
A0006281biological_processDNA repair
A0006289biological_processnucleotide-excision repair
A0006511biological_processubiquitin-dependent protein catabolic process
A0006974biological_processDNA damage response
A0007056biological_processspindle assembly involved in female meiosis
A0007283biological_processspermatogenesis
A0008283biological_processcell population proliferation
A0010498biological_processproteasomal protein catabolic process
A0010506biological_processregulation of autophagy
A0016567biological_processprotein ubiquitination
A0019076biological_processviral release from host cell
A0030174biological_processregulation of DNA-templated DNA replication initiation
A0030674molecular_functionprotein-macromolecule adaptor activity
A0031297biological_processreplication fork processing
A0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
A0031465cellular_componentCul4B-RING E3 ubiquitin ligase complex
A0032814biological_processregulation of natural killer cell activation
A0032991cellular_componentprotein-containing complex
A0034644biological_processcellular response to UV
A0035861cellular_componentsite of double-strand break
A0040029biological_processepigenetic regulation of gene expression
A0042127biological_processregulation of cell population proliferation
A0042752biological_processregulation of circadian rhythm
A0042981biological_processregulation of apoptotic process
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0044725biological_processepigenetic programming in the zygotic pronuclei
A0044877molecular_functionprotein-containing complex binding
A0045070biological_processpositive regulation of viral genome replication
A0045722biological_processpositive regulation of gluconeogenesis
A0045732biological_processpositive regulation of protein catabolic process
A0045995biological_processregulation of embryonic development
A0046726biological_processpositive regulation by virus of viral protein levels in host cell
A0051702biological_processbiological process involved in interaction with symbiont
A0060964biological_processregulation of miRNA-mediated gene silencing
A0070062cellular_componentextracellular exosome
A0070914biological_processUV-damage excision repair
A0071987molecular_functionWD40-repeat domain binding
A0080008cellular_componentCul4-RING E3 ubiquitin ligase complex
A0080135biological_processregulation of cellular response to stress
A0097602molecular_functioncullin family protein binding
A0160072molecular_functionubiquitin ligase complex scaffold activity
A1901987biological_processregulation of cell cycle phase transition
A1901990biological_processregulation of mitotic cell cycle phase transition
A1902412biological_processregulation of mitotic cytokinesis
A1904178biological_processnegative regulation of adipose tissue development
A2000036biological_processregulation of stem cell population maintenance
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0016020cellular_componentmembrane
B0016567biological_processprotein ubiquitination
B0030177biological_processpositive regulation of Wnt signaling pathway
B0031333biological_processnegative regulation of protein-containing complex assembly
B0031334biological_processpositive regulation of protein-containing complex assembly
B0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
B0031465cellular_componentCul4B-RING E3 ubiquitin ligase complex
B0034766biological_processnegative regulation of monoatomic ion transmembrane transport
B0035641biological_processlocomotory exploration behavior
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0044325molecular_functiontransmembrane transporter binding
B0048471cellular_componentperinuclear region of cytoplasm
B1990756molecular_functionubiquitin-like ligase-substrate adaptor activity
C0000082biological_processG1/S transition of mitotic cell cycle
C0000086biological_processG2/M transition of mitotic cell cycle
C0000287molecular_functionmagnesium ion binding
C0000307cellular_componentcyclin-dependent protein kinase holoenzyme complex
C0000781cellular_componentchromosome, telomeric region
C0000793cellular_componentcondensed chromosome
C0000805cellular_componentX chromosome
C0000806cellular_componentY chromosome
C0004672molecular_functionprotein kinase activity
C0004674molecular_functionprotein serine/threonine kinase activity
C0004693molecular_functioncyclin-dependent protein serine/threonine kinase activity
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005634cellular_componentnucleus
C0005635cellular_componentnuclear envelope
C0005654cellular_componentnucleoplasm
C0005667cellular_componenttranscription regulator complex
C0005737cellular_componentcytoplasm
C0005768cellular_componentendosome
C0005813cellular_componentcentrosome
C0005829cellular_componentcytosol
C0006260biological_processDNA replication
C0006338biological_processchromatin remodeling
C0006468biological_processprotein phosphorylation
C0007099biological_processcentriole replication
C0007165biological_processsignal transduction
C0007265biological_processRas protein signal transduction
C0007346biological_processregulation of mitotic cell cycle
C0008284biological_processpositive regulation of cell population proliferation
C0015030cellular_componentCajal body
C0016301molecular_functionkinase activity
C0018105biological_processpeptidyl-serine phosphorylation
C0019904molecular_functionprotein domain specific binding
C0030332molecular_functioncyclin binding
C0031453biological_processpositive regulation of heterochromatin formation
C0031571biological_processmitotic G1 DNA damage checkpoint signaling
C0035173molecular_functionhistone kinase activity
C0036064cellular_componentciliary basal body
C0043247biological_processtelomere maintenance in response to DNA damage
C0043687biological_processpost-translational protein modification
C0045740biological_processpositive regulation of DNA replication
C0051298biological_processcentrosome duplication
C0051321biological_processmeiotic cell cycle
C0071732biological_processcellular response to nitric oxide
C0090398biological_processcellular senescence
C0097123cellular_componentcyclin A1-CDK2 complex
C0097124cellular_componentcyclin A2-CDK2 complex
C0097134cellular_componentcyclin E1-CDK2 complex
C0097135cellular_componentcyclin E2-CDK2 complex
C0097472molecular_functioncyclin-dependent protein kinase activity
C0106310molecular_functionprotein serine kinase activity
C0120186biological_processnegative regulation of protein localization to chromatin
C0120261biological_processregulation of heterochromatin organization
C1905784biological_processregulation of anaphase-promoting complex-dependent catabolic process
Functional Information from PROSITE/UniProt
site_idPS00107
Number of Residues24
DetailsPROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. IGEGTYGVVYkArnkltgev..........VALK
ChainResidueDetails
CILE10-LYS33
site_idPS00108
Number of Residues13
DetailsPROTEIN_KINASE_ST Serine/Threonine protein kinases active-site signature. VlHrDLKpqNLLI
ChainResidueDetails
CVAL123-ILE135
site_idPS00292
Number of Residues32
DetailsCYCLINS Cyclins signature. RaiLldWLmevcevykLhretFylAQdFFDRY
ChainResidueDetails
DARG145-TYR176
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues46
DetailsRepeat: {"description":"WD 1","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues45
DetailsRepeat: {"description":"WD 2","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues51
DetailsRepeat: {"description":"WD 3","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues52
DetailsRepeat: {"description":"WD 4","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues44
DetailsRepeat: {"description":"WD 5","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues52
DetailsRepeat: {"description":"WD 6","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues46
DetailsRepeat: {"description":"WD 7","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues36
DetailsRepeat: {"description":"WD 8","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues87
DetailsRepeat: {"description":"WD 16","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues60
DetailsRepeat: {"description":"WD 17","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues39
DetailsRepeat: {"description":"WD 18","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues42
DetailsRepeat: {"description":"WD 19","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues51
DetailsRepeat: {"description":"WD 20","evidences":[{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues342
DetailsRegion: {"description":"WD40 beta-propeller A"}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues36
DetailsRegion: {"description":"WD40 beta-propeller C"}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues1
DetailsModified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI18
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q9ESW0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI19
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI20
Number of Residues238
DetailsDomain: {"description":"Lon N-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU01123","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI21
Number of Residues108
DetailsDomain: {"description":"CULT","evidences":[{"source":"PROSITE-ProRule","id":"PRU01124","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI22
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"25108355","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"41565821","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TZ4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OTY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9OUL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9SFM","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI23
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"25108355","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TZ4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI24
Number of Residues1
DetailsActive site: {"description":"Proton acceptor"}
ChainResidueDetails
site_idSWS_FT_FI25
Number of Residues16
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00159","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"17095507","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21565702","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI26
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"41100585","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9I9J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9I9K","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI27
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"41100585","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9I9K","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI28
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"21565702","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI29
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"21565702","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"41100585","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"9I9K","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"9QCV","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI30
Number of Residues3
DetailsSite: {"description":"CDK7 binding","evidences":[{"source":"PubMed","id":"17373709","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI31
Number of Residues1
DetailsModified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI32
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"1396589","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17095507","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI33
Number of Residues1
DetailsModified residue: {"description":"Phosphotyrosine; by WEE1","evidences":[{"source":"PubMed","id":"1396589","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17095507","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI34
Number of Residues1
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI35
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine; by CAK and CCRK","evidences":[{"source":"PubMed","id":"1396589","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14597612","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16325401","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17095507","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17570665","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20147522","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20360007","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21565702","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"41100585","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28666995","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI36
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18691976","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19369195","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

259987

PDB entries from 2026-09-23

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