8TK2

HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed with 2-((2,4-difluorobenzyl)amino)-2-oxoacetic acid

• PDB DOI: https://doi.org/10.2210/pdb8TK2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• 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: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) binding 2-((2,4-difluorobenzyl)amino)-2-oxoacetic acid

Aleshin, A.E., Cosford, N., 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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.18 kDa 
• Atom Count: 3,211 
• Modelled Residue Count: 360 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase 3	A, B	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I1Y (Subject of Investigation/LOI)	C [auth A], D [auth B]	{[(2,4-difluorophenyl)methyl]amino}(oxo)acetic acid C9 H7 F2 N O3 YQDORBOSJQHAGW-UHFFFAOYSA-N
PEG	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	E [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.536	α = 78.07
b = 44.328	β = 89.99
c = 59.863	γ = 81.69

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	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