8C3Q

Crystal structure of DYRK1A in complex with rutin

• PDB DOI: https://doi.org/10.2210/pdb8C3Q/pdb

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


• Deposited: 2022-12-28 Released: 2024-01-10 
• Deposition Author(s): Grygier, P., Pustelny, K., Dubin, G., Czarna, A.
• Funding Organization(s): Polish National Science Centre, National Center for Research and Development (Poland)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.210 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Crystal structure of DYRK1A in complex with rutin

Grygier, P., Pustelny, K., Dubin, G., Czarna, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.58 kDa 
• Atom Count: 5,746 
• Modelled Residue Count: 688 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B	370	Homo sapiens	Mutation(s): 0  Gene Names: DYRK1A, DYRK, MNB, MNBH 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RUT (Subject of Investigation/LOI)	C [auth A], D [auth B]	RUTIN C27 H30 O16 IKGXIBQEEMLURG-NVPNHPEKSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.210 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.187	α = 90
b = 134.187	β = 90
c = 91.15	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Grygier, P., Pustelny, K., Dubin, G., Czarna, A.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2019/34/E/NZ1/00467
National Center for Research and Development (Poland)	Poland	PPN/PPO/2018/1/00046

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary