Macromolecule Content

Total Structure Weight: 45.59 kDa
Atom Count: 3010
Residue Count: 333
Unique protein chains: 2

4ROJ

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

DOI: 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.219
R-Value Work: 0.186
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

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.

Macromolecules

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(by identity cutoff) | Structure

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
Find proteins for P52735 (Homo sapiens) Explore P52735 Go to UniProtKB: P52735
NIH Common Fund Data Resources
PHAROS: P52735 GTEx: ENSG00000160293
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-interacting protein	D, E, F	14	Homo sapiens	Mutation(s): 2 Gene Names: TXNIP, VDUP1
Find proteins for Q9H3M7 (Homo sapiens) Explore Q9H3M7 Go to UniProtKB: Q9H3M7
NIH Common Fund Data Resources
PHAROS: Q9H3M7 GTEx: ENSG00000265972
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain H [A] SDF format, chain I [A] SDF format, chain J [A] SDF format, chain K [B] SDF format, chain L [B] SDF format, chain M [B] SDF format, chain N [B] SDF format, chain O [B] SDF format, chain P [C] SDF format, chain Q [C] SDF format, chain R [C] SDF format, chain S [C] SDF format, chain T [F] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain I [A] MOL2 format, chain J [A] MOL2 format, chain K [B] MOL2 format, chain L [B] MOL2 format, chain M [B] MOL2 format, chain N [B] MOL2 format, chain O [B] MOL2 format, chain P [C] MOL2 format, chain Q [C] MOL2 format, chain R [C] MOL2 format, chain S [C] MOL2 format, chain T [F]	A, B, C, F	UNKNOWN ATOM OR ION X		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on 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
R-Value Work: 0.186
R-Value Observed: 0.187
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-10-28
Released Date: 2014-12-10

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History

Version 1.0: 2014-12-10
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.