6NFA | pdb_00006nfa

Vav1 inhibited by an allosteric inhibitor: Vav1 inhibitors block GEF activity

• PDB DOI: https://doi.org/10.2210/pdb6NFA/pdb

• Classification: SIGNALING PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-19 Released: 2019-12-25 
• Deposition Author(s): Knapp, M.S., Elling, R.A., Ornelas, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Allosteric Inhibitors of VAV1 Block Guanine Nucleotide Exchange Activity

Gerspacher, M., Skaanderup, P.R.

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: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 50.17 kDa 
• Atom Count: 3,243 
• Modeled Residue Count: 386 
• Deposited Residue Count: 421 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene vav	A	421	Homo sapiens	Mutation(s): 0  Gene Names: VAV1, VAV
UniProt & NIH Common Fund Data Resources
Find proteins for P15498 (Homo sapiens) Explore P15498  Go to UniProtKB:  P15498
PHAROS:  P15498 GTEx:  ENSG00000141968

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9K1	D [auth A]	(2S)-2-{[3-(4-methylphenyl)imidazo[1,2-a]pyrazin-8-yl]amino}-3-(pyridin-3-yl)propan-1-ol C21 H21 N5 O ALAPXRDQVUXCMS-SFHVURJKSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.88	α = 90
b = 67.641	β = 90
c = 179.544	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Knapp, M.S., Elling, R.A., Ornelas, E.

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description