6YF8 | pdb_00006yf8

DYRK1A with PST001

• PDB DOI: https://doi.org/10.2210/pdb6YF8/pdb

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


• Deposited: 2020-03-26 Released: 2021-04-07 
• Deposition Author(s): Rothweiler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

DYRK1A with PST001

Rothweiler, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 171.81 kDa 
• Atom Count: 11,014 
• Modeled Residue Count: 1,346 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B, C, D	368	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
OPW (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	~{N}-[5-(5-methoxy-1,3-benzothiazol-2-yl)pyridin-3-yl]ethanamide C15 H13 N3 O2 S JLUXIHDOQQZMIZ-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
OPW	BindingDB:  6YF8	IC50: min: 51, max: 335 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88	α = 90
b = 88.04	β = 90
c = 229.72	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Rothweiler, U.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary