8TK3

HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) having oxidized catalytic cysteine and complexed with 6-(difluoromethyl)pyrimidin-4-ol at two allosteric sites

• PDB DOI: https://doi.org/10.2210/pdb8TK3/pdb

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


• Deposited: 2023-07-25 Released: 2024-08-14 
• Deposition Author(s): Aleshin, A.E., Wu, J., Lambert, L.J., Cosford, N.D.P., Tautz, L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) having oxidized catalytic cysteine and complexed with 6-(difluoromethyl)pyrimidin-4-ol at two allosteric sites

Aleshin, A.E., Wu, J., Lambert, L.J., Cosford, N.D.P., Tautz, L.

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)

Macromolecule Content

• Total Structure Weight: 20.84 kDa 
• Atom Count: 1,581 
• Modelled Residue Count: 179 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase 3	A	183	Homo sapiens	Mutation(s): 0  Gene Names: DUSP3, VHR EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P51452 (Homo sapiens) Explore P51452  Go to UniProtKB:  P51452
PHAROS:  P51452 GTEx:  ENSG00000108861

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I2X (Subject of Investigation/LOI)	B [auth A], C [auth A]	6-(difluoromethyl)pyrimidin-4-ol C5 H4 F2 N2 O CRXWFHCGXRAVCL-UHFFFAOYSA-N
DMS	D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.133	α = 90
b = 52.467	β = 90
c = 100.493	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Aleshin, A.E., Wu, J., Lambert, L.J., Cosford, N.D.P., Tautz, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R21 AI160161

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release