Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


The structure of human beta-defensin-2 shows evidence of higher order oligomerization.

Hoover, D.M.Rajashankar, K.R.Blumenthal, R.Puri, A.Oppenheim, J.J.Chertov, O.Lubkowski, J.

(2000) J Biol Chem 275: 32911-32918

  • DOI: https://doi.org/10.1074/jbc.M006098200
  • Primary Citation of Related Structures:  
    1FD3, 1FD4

  • PubMed Abstract: 

    Defensins are small cationic peptides that are crucial components of innate immunity, serving as both antimicrobial agents and chemoattractant molecules. The specific mechanism of antimicrobial activity involves permeabilization of bacterial membranes. It has been postulated that individual monomers oligomerize to form a pore through anionic membranes, although the evidence is only indirect. Here, we report two high resolution x-ray structures of human beta-defensin-2 (hBD2). The phases were experimentally determined by the multiwavelength anomalous diffraction method, utilizing a novel, rapid method of derivatization with halide ions. Although the shape and charge distribution of the monomer are similar to those of other defensins, an additional alpha-helical region makes this protein topologically distinct from the mammalian alpha- and beta-defensin structures reported previously. hBD2 forms dimers topologically distinct from that of human neutrophil peptide-3. The quaternary octameric arrangement of hBD2 is conserved in two crystal forms. These structures provide the first detailed description of dimerization of beta-defensins, and we postulate that the mode of dimerization of hBD2 is representative of other beta-defensins. The structural and electrostatic properties of the hBD2 octamer support an electrostatic charge-based mechanism of membrane permeabilization by beta-defensins, rather than a mechanism based on formation of bilayer-spanning pores.

  • Organizational Affiliation

    Macromolecular Crystallography Laboratory, Program in Structural Biology, NCI-Frederick Cancer Research and Development Center, National Institutes of Health, Frederick, Maryland 21702, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
41N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O15263 (Homo sapiens)
Explore O15263 
Go to UniProtKB:  O15263
PHAROS:  O15263
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15263
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.05α = 90
b = 103.91β = 90
c = 28.27γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
DMmodel building
ARPmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance