4ROJ | pdb_00004roj

Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide

• PDB DOI: https://doi.org/10.2210/pdb4ROJ/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-10-28 Released: 2014-12-10 
• Deposition Author(s): Liu, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.219 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide

Liu, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.59 kDa 
• Atom Count: 3,010 
• Modeled Residue Count: 333 
• Deposited Residue Count: 393 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide exchange factor VAV2	A, B, C	117	Homo sapiens	Mutation(s): 0  Gene Names: VAV2
UniProt & NIH Common Fund Data Resources
Find proteins for P52735 (Homo sapiens) Explore P52735  Go to UniProtKB:  P52735
PHAROS:  P52735 GTEx:  ENSG00000160293

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-interacting protein	D, E, F	14	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3M7 (Homo sapiens) Explore Q9H3M7  Go to UniProtKB:  Q9H3M7
PHAROS:  Q9H3M7 GTEx:  ENSG00000265972

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth F]	UNKNOWN ATOM OR ION X

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.219 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.764	α = 90
b = 99.764	β = 90
c = 160.946	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Liu, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-10-30
  Changes: Structure summary