2VX3

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

Structural Biology Knowledgebase: 2VX3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VX3

Classification: TRANSFERASE

Total Structure Weight: 183316.91

Macromolecule Entities
Molecule Chains Length Organism Details
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A A, B, C, D 382 Homo sapiens EC#: 2.7.12.1 IUBMB
Fragment: RESIDUES 127-485
Gene Name(s): DYRK1A Gene View DYRK MNB MNBH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
D15
Query on D15

A, B, C, D N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}- 1H-indazol-3-yl)benzamide
C24 H22 Cl N5 O2
JDGOPNUGILVNJZ-IBGZPJMESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
P6G
Query on P6G

A, B, C, D HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400 (Synonym)
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PTR
Query on PTR
A, B, C, D L-PEPTIDE LINKING C9 H12 N O6 P TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.185
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 264.20 α = 90.00
b = 65.11 β = 115.44
c = 140.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-30
  • Released Date: 2008-09-16
  • Deposition author(s): Roos, A.K., Soundararajan, M., Pike, A.C.W., Federov, O., King, O., Burgess-Brown, N., Philips, C., Filippakopoulos, P., Arrowsmith, C.H., Wikstrom, M., Edwards, A., von Delft, F., Bountra, C., Knapp, S.

Revision History

  • 2013-06-26
    Type: Citation | Details: JRNL
  • 2013-06-26
    Type: Biological assembly | Details: REMARK 350
  • 2012-12-05
    Type: Citation | Details: JRNL
  • 2012-12-05
    Type: Sequence database correspondence | Details: SEQADV, DBREF
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4