3I5W

Crystal structure of human alpha-defensin 5 (mutant R13H)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective arginines are important for the antibacterial activity and host cell interaction of human alpha-defensin 5

de Leeuw, E.Rajabi, M.Zou, G.Pazgier, M.Lu, W.

(2009) Febs Lett. 583: 2507-2512

  • DOI: 10.1016/j.febslet.2009.06.051

  • PubMed Abstract: 
  • Defensins constitute a major family of natural antimicrobial peptides that protect the host against microbial invasion. Here, we report on the antibacterial properties and cellular interaction of Human Defensin 5 as a function of its positive charge ...

    Defensins constitute a major family of natural antimicrobial peptides that protect the host against microbial invasion. Here, we report on the antibacterial properties and cellular interaction of Human Defensin 5 as a function of its positive charge and hydrophobicity. We find that selective replacement of arginine residues in HD-5 by alanine or charge-neutral lysine residues reduces antibacterial killing as well as host cell interaction. We identify arginines at positions 9 and 28 in the HD-5 sequence as particularly important for its function. Replacement of arginine at position 13 to Histidine, as observed in a Crohn's disease patient, reduced bacterial killing strain-selectively. Finally, we find that HD-5 interacts with host cells via receptor-mediated mechanisms.


    Organizational Affiliation

    University of Maryland Baltimore School of Medicine, Institute of Human Virology, Department of Biochemistry and Molecular Biology, Baltimore, MD 21201, USA. edeleeuw2@ihv.umaryland.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Defensin-5
A, B
32Homo sapiensMutation(s): 1 
Gene Names: DEFA5 (DEF5)
Find proteins for Q01523 (Homo sapiens)
Go to Gene View: DEFA5
Go to UniProtKB:  Q01523
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 48.018α = 90.00
b = 49.754β = 90.00
c = 62.355γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-07-06 
  • Released Date: 2009-07-28 
  • Deposition Author(s): Pazgier, M., Lu, W.

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2012-04-11
    Type: Derived calculations