2VX3 | pdb_00002vx3

Crystal structure of the human dual specificity tyrosine- phosphorylation-regulated kinase 1A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.230 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2VX3

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structures of Down Syndrome Kinases, Dyrks, Reveal Mechanisms of Kinase Activation and Substrate Recognition.

Soundararajan, M.Roos, A.K.Savitsky, P.Filippakopoulos, P.Kettenbach, A.N.Olsen, J.V.Gerber, S.A.Eswaran, J.Knapp, S.Elkins, J.M.

(2013) Structure 21: 986

  • DOI: https://doi.org/10.1016/j.str.2013.03.012
  • Primary Citation Related Structures: 
    2VX3, 2WO6, 3K2L

  • PubMed Abstract: 

    Dual-specificity tyrosine-(Y)-phosphorylation-regulated kinases (DYRKs) play key roles in brain development, regulation of splicing, and apoptosis, and are potential drug targets for neurodegenerative diseases and cancer. We present crystal structures of one representative member of each DYRK subfamily: DYRK1A with an ATP-mimetic inhibitor and consensus peptide, and DYRK2 including NAPA and DH (DYRK homology) box regions. The current activation model suggests that DYRKs are Ser/Thr kinases that only autophosphorylate the second tyrosine of the activation loop YxY motif during protein translation. The structures explain the roles of this tyrosine and of the DH box in DYRK activation and provide a structural model for DYRK substrate recognition. Phosphorylation of a library of naturally occurring peptides identified substrate motifs that lack proline in the P+1 position, suggesting that DYRK1A is not a strictly proline-directed kinase. Our data also show that DYRK1A wild-type and Y321F mutant retain tyrosine autophosphorylation activity.


  • Organizational Affiliation
    • Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.

Macromolecule Content 

  • Total Structure Weight: 183.32 kDa 
  • Atom Count: 11,571 
  • Modeled Residue Count: 1,370 
  • Deposited Residue Count: 1,528 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
A, B, C, D
382Homo sapiensMutation(s): 0 
EC: 2.7.12.1 (PDB Primary Data), 2.7.11.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens)
Explore Q13627 
Go to UniProtKB:  Q13627
PHAROS:  Q13627
GTEx:  ENSG00000157540 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13627
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D15

Query on D15



Download:Ideal Coordinates CCD File
AA [auth D],
E [auth A],
K [auth B],
T [auth C]
N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}-1H-indazol-3-yl)benzamide
C24 H22 Cl N5 O2
JDGOPNUGILVNJZ-IBGZPJMESA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
CA [auth D]
G [auth A]
H [auth A]
I [auth A]
M [auth B]
CA [auth D],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
V [auth C]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
DA [auth D]
J [auth A]
P [auth B]
Q [auth B]
R [auth B]
DA [auth D],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
W [auth C],
X [auth C],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
BA [auth D]
EA [auth D]
F [auth A]
FA [auth D]
L [auth B]
BA [auth D],
EA [auth D],
F [auth A],
FA [auth D],
L [auth B],
S [auth B],
U [auth C],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.203α = 90
b = 65.105β = 115.44
c = 140.282γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-12-05
    Changes: Database references
  • Version 1.3: 2013-06-26
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary