6HDP

Human DYRK2 bound to Scorzodihydrostilbene A

• PDB DOI: https://doi.org/10.2210/pdb6HDP/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-18 Released: 2019-08-28 
• Deposition Author(s): Elkins, J.M., Soundararajan, M., Proksch, P., Meijer, L., Vollmar, M., Krojer, T., Bountra, C., Edwards, A.M., Arrowsmith, C., Knapp, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

DYRK2 bound to Scorzodihydrostilbene A

Elkins, J.M., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.01 kDa 
• Atom Count: 3,498 
• Modelled Residue Count: 409 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 2	A	429	Homo sapiens	Mutation(s): 0  Gene Names: DYRK2 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92630 (Homo sapiens) Explore Q92630  Go to UniProtKB:  Q92630
PHAROS:  Q92630 GTEx:  ENSG00000127334

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FZ5	B [auth A]	Scorzodihydrostilbene A C23 H28 O10 YRCZOJOYJCLBDV-DODNOZFWSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.527	α = 90
b = 84.527	β = 90
c = 148.372	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Elkins, J.M., Soundararajan, M., Proksch, P., Meijer, L., Vollmar, M., Krojer, T., Bountra, C., Edwards, A.M., Arrowsmith, C., Knapp, S.

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary