4BBM

CRYSTAL STRUCTURE OF THE HUMAN CDKL2 KINASE DOMAIN WITH BOUND TCS 2312


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function.

Canning, P.Park, K.Goncalves, J.Li, C.Howard, C.J.Sharpe, T.D.Holt, L.J.Pelletier, L.Bullock, A.N.Leroux, M.R.

(2018) Cell Rep 22: 885-894

  • DOI: https://doi.org/10.1016/j.celrep.2017.12.083
  • Primary Citation of Related Structures:  
    3ZDU, 4AAA, 4AGU, 4BBM, 4BGQ

  • PubMed Abstract: 

    Various kinases, including a cyclin-dependent kinase (CDK) family member, regulate the growth and functions of primary cilia, which perform essential roles in signaling and development. Neurological disorders linked to CDK-Like (CDKL) proteins suggest that these underexplored kinases may have similar functions. Here, we present the crystal structures of human CDKL1, CDKL2, CDKL3, and CDKL5, revealing their evolutionary divergence from CDK and mitogen-activated protein kinases (MAPKs), including an unusual ?J helix important for CDKL2 and CDKL3 activity. C. elegans CDKL-1, most closely related to CDKL1-4 and localized to neuronal cilia transition zones, modulates cilium length; this depends on its kinase activity and ?J helix-containing C terminus. Human CDKL5, linked to Rett syndrome, also localizes to cilia, and it impairs ciliogenesis when overexpressed. CDKL5 patient mutations modeled in CDKL-1 cause localization and/or cilium length defects. Together, our studies establish a disease model system suggesting cilium length defects as a pathomechanism for neurological disorders, including epilepsy.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE-LIKE 2
A, B
331Homo sapiensMutation(s): 2 
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q92772 (Homo sapiens)
Explore Q92772 
Go to UniProtKB:  Q92772
PHAROS:  Q92772
GTEx:  ENSG00000138769 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92772
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TC0
Query on TC0

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
4'-[5-[[3-[(CYCLOPROPYLAMINO)METHYL]PHENYL]AMINO]-1H-PYRAZOL-3-YL]-[1,1'-BIPHENYL]-2,4-DIOL
C25 H24 N4 O2
GRGYFHNWICGOLR-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.583α = 71.53
b = 68.047β = 89.92
c = 82.343γ = 88.97
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references, Structure summary
  • Version 1.2: 2022-03-30
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Refinement description