6BNM | pdb_00006bnm

Crystal Structure of the P-Rex2 PH domain

• PDB DOI: https://doi.org/10.2210/pdb6BNM/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-11-17 Released: 2018-11-21 
• Deposition Author(s): Cash, J.N., Sharma, P.V., Tesmer, J.J.G.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), American Cancer Society-Michigan Cancer Research Fund

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.232 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structural and biochemical characterization of the pleckstrin homology domain of the RhoGEF P-Rex2 and its regulation by PIP3.

Cash, J.N., Sharma, P.V., Tesmer, J.J.G.

(2019) J Struct Biol 1

• DOI: https://doi.org/10.1016/j.yjsbx.2018.100001

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

Macromolecule Content 

• Total Structure Weight: 19.21 kDa 
• Atom Count: 1,213 
• Modeled Residue Count: 137 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein	A	162	Homo sapiens	Mutation(s): 0  Gene Names: PREX2, DEPDC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q70Z35 (Homo sapiens) Explore Q70Z35  Go to UniProtKB:  Q70Z35
PHAROS:  Q70Z35 GTEx:  ENSG00000046889

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.232 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.105	α = 90
b = 60.105	β = 90
c = 86.238	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Cash, J.N., Sharma, P.V., Tesmer, J.J.G.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL086865
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL122416
American Cancer Society-Michigan Cancer Research Fund	United States	PF-14-224-01-DMC

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description