3LOE

Crystal structure of human alpha-defensin 1 (F28A mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Trp-26 imparts functional versatility to human alpha-defensin HNP1.

Wei, G.Pazgier, M.de Leeuw, E.Rajabi, M.Li, J.Zou, G.Jung, G.Yuan, W.Lu, W.Y.Lehrer, R.I.Lu, W.

(2010) J.Biol.Chem. 285: 16275-16285

  • DOI: 10.1074/jbc.M110.102749
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We performed a comprehensive alanine scan of human alpha-defensin HNP1 and tested the ability of the resulting analogs to kill Staphylococcus aureus, inhibit anthrax lethal factor, and bind human immunodeficiency virus-1 gp120. By far, the most delet ...

    We performed a comprehensive alanine scan of human alpha-defensin HNP1 and tested the ability of the resulting analogs to kill Staphylococcus aureus, inhibit anthrax lethal factor, and bind human immunodeficiency virus-1 gp120. By far, the most deleterious mutation for all of these functions was W26A. The activities lost by W26A-HNP1 were restored progressively by replacing W26 with non-coded, straight-chain aliphatic amino acids of increasing chain length. The hydrophobicity of residue 26 also correlated with the ability of the analogs to bind immobilized wild type HNP1 and to undergo further self-association. Thus, the hydrophobicity of residue 26 is not only a key determinant of the direct interactions of HNP1 with target molecules, but it also governs the ability of this peptide to form dimers and more complex quaternary structures at micromolar concentrations. Although all defensin peptides are cationic, their amphipathicity is at least as important as their positive charge in enabling them to participate in innate host defense.


    Organizational Affiliation

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil defensin 1
A
30Homo sapiensMutation(s): 1 
Gene Names: DEFA1, DEFA1B (DEF1, DEFA2, MRS)
Find proteins for P59665 (Homo sapiens)
Go to Gene View: DEFA1 DEFA1B
Go to UniProtKB:  P59665
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.174 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 31.527α = 90.00
b = 39.827β = 90.00
c = 46.259γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-02-03 
  • Released Date: 2010-03-09 
  • Deposition Author(s): Pazgier, M., Lu, W.

Revision History 

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance