1H6H

Structure of the PX domain from p40phox bound to phosphatidylinositol 3-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of the Px Domain from P40Phox Bound to Phosphatidylinositol 3-Phosphate

Bravo, J.Karathanassis, D.Pacold, C.M.Pacold, M.E.Ellson, C.D.Anderson, K.E.Butler, J.G.Lavenir, I.Perisic, O.Hawkins, P.T.Stephens, L.Williams, R.L.

(2001) Mol.Cell 8: 829


  • PubMed Abstract: 
  • More than 50 human proteins with a wide range of functions have a 120 residue phosphoinositide binding module known as the PX domain. The 1.7 A X-ray crystal structure of the PX domain from the p40(phox) subunit of NADPH oxidase bound to PtdIns(3)P s ...

    More than 50 human proteins with a wide range of functions have a 120 residue phosphoinositide binding module known as the PX domain. The 1.7 A X-ray crystal structure of the PX domain from the p40(phox) subunit of NADPH oxidase bound to PtdIns(3)P shows that the PX domain embraces the 3-phosphate on one side of a water-filled, positively charged pocket and reveals how 3-phosphoinositide specificity is achieved. A chronic granulomatous disease (CGD)-associated mutation in the p47(phox) PX domain that abrogates PtdIns(3)P binding maps to a conserved Arg that does not directly interact with the phosphoinositide but instead appears to stabilize a critical lipid binding loop. The SH3 domain present in the full-length protein does not affect soluble PtdIns(3)P binding to the p40(phox) PX domain.


    Related Citations: 
    • Solution Structure of the Px Domain, a Target of the SH3 Domain
      Hiroaki, H.,Ago, T.,Ito, T.,Sumimoto, H.,Kohda, D.
      (2001) Nat.Struct.Mol.Biol. 8: 526


    Organizational Affiliation

    Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 2QH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUTROPHIL CYTOSOL FACTOR 4
A
143Homo sapiensGene Names: NCF4 (SH3PXD4)
Find proteins for Q15080 (Homo sapiens)
Go to Gene View: NCF4
Go to UniProtKB:  Q15080
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIB
Query on PIB

Download SDF File 
Download CCD File 
A
2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATED (+)-SN-1,2-DI-O-BUTANOYLGLYCERYL,3-O-PHOSPHO
C17 H32 O16 P2
NKJZZWLREOAJGO-HODIZBBFSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PIBKd: 5000 nM BINDINGMOAD
PIBKd: 5000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 96.760α = 90.00
b = 33.642β = 132.42
c = 76.430γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHARPphasing
CNSrefinement
SCALAdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Source and taxonomy