1H6H

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

• PDB DOI:  https://doi.org/10.2210/pdb1H6H/pdb

• Classification: PX DOMAIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2001-06-15 Released: 2001-11-01 
• Deposition Author(s): Karathanassis, D., Bravo, J., Pacold, M., Perisic, O., Williams, R.L.

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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 

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: 11684018 
• DOI: https://doi.org/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. 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 16.96 kDa 
• Atom Count: 1,373 
• Modelled Residue Count: 143 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTROPHIL CYTOSOL FACTOR 4	A	143	Homo sapiens	Mutation(s): 0  Gene Names: NCF4, SH3PXD4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q15080 (Homo sapiens) Explore Q15080  Go to UniProtKB:  Q15080
PHAROS:  Q15080

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PIB	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
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 96.76	α = 90
b = 33.642	β = 132.42
c = 76.43	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-01 
Deposition Author(s): Karathanassis, D., Bravo, J., Pacold, M., Perisic, O., Williams, R.L.

Revision History  

• 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