1H6H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


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

  • DOI: 10.1016/s1097-2765(01)00372-0
  • Primary Citation of Related Structures:  
    1H6H

  • 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 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 ...

    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 Biol 8: 526

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEUTROPHIL CYTOSOL FACTOR 4A143Homo sapiensMutation(s): 0 
Gene Names: NCF4SH3PXD4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15080 (Homo sapiens)
Explore Q15080 
Go to UniProtKB:  Q15080
PHAROS:  Q15080
GTEx:  ENSG00000100365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15080
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIB
Query on PIB

Download Ideal Coordinates CCD File 
B [auth A]2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
C17 H32 O16 P2
NKJZZWLREOAJGO-HODIZBBFSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PIB Binding MOAD:  1H6H Kd: 5000 (nM) from 1 assay(s)
PDBBind:  1H6H Kd: 5000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.76α = 90
b = 33.642β = 132.42
c = 76.43γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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