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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9H59

Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7

This is a non-PDB format compatible entry.
Functional Information from GO Data
ChainGOidnamespacecontents
A0000781cellular_componentchromosome, telomeric region
A0003676molecular_functionnucleic acid binding
A0003677molecular_functionDNA binding
A0003684molecular_functiondamaged DNA binding
A0005515molecular_functionprotein binding
A0005615cellular_componentextracellular space
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
A0048511biological_processrhythmic process
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
B0034766biological_processnegative regulation of monoatomic ion transmembrane transport
B0035641biological_processlocomotory exploration behavior
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0044325molecular_functiontransmembrane transporter binding
B0046872molecular_functionmetal ion binding
B0048471cellular_componentperinuclear region of cytoplasm
B0060173biological_processlimb development
C0000166molecular_functionnucleotide binding
C0000922cellular_componentspindle pole
C0004672molecular_functionprotein kinase activity
C0004674molecular_functionprotein serine/threonine kinase activity
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0005813cellular_componentcentrosome
C0005815cellular_componentmicrotubule organizing center
C0005874cellular_componentmicrotubule
C0006468biological_processprotein phosphorylation
C0007346biological_processregulation of mitotic cell cycle
C0016301molecular_functionkinase activity
C0016740molecular_functiontransferase activity
C0032206biological_processpositive regulation of telomere maintenance
C0033044biological_processregulation of chromosome organization
C0035865biological_processcellular response to potassium ion
C0043549biological_processregulation of kinase activity
C0046872molecular_functionmetal ion binding
C0051225biological_processspindle assembly
C0106310molecular_functionprotein serine kinase activity
C0140677molecular_functionmolecular function activator activity
C1900227biological_processpositive regulation of NLRP3 inflammasome complex assembly
Functional Information from PROSITE/UniProt
site_idPS00107
Number of Residues24
DetailsPROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. IGRGQFSEVYrAaclldgvp..........VALK
ChainResidueDetails
CILE40-LYS63
site_idPS00108
Number of Residues13
DetailsPROTEIN_KINASE_ST Serine/Threonine protein kinases active-site signature. VmHrDIKpaNVFI
ChainResidueDetails
CVAL157-ILE169
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues766
DetailsRegion: {"description":"Interaction with CDT1","evidences":[{"source":"PubMed","id":"15448697","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues343
DetailsRegion: {"description":"WD repeat beta-propeller A"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues316
DetailsRegion: {"description":"WD repeat beta-propeller B; Interaction with CUL4A"}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues1
DetailsModified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q9ESW0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI7
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_FI8
Number of Residues265
DetailsDomain: {"description":"Protein kinase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00159","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues1
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU00159","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10027","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues9
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"19941817","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2WQN","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues1
DetailsSite: {"description":"Autoinhibitory","evidences":[{"source":"PubMed","id":"19941817","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine; by NEK9","evidences":[{"source":"PubMed","id":"12840024","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26522158","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues108
DetailsDomain: {"description":"CULT","evidences":[{"source":"PROSITE-ProRule","id":"PRU01124","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues7
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"25108355","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TZ4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

247536

PDB entries from 2026-01-14

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