Crystal structure of human beta-defensin 2 in complex with PIP2

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Human beta-defensin 2 killsCandida albicansthrough phosphatidylinositol 4,5-bisphosphate-mediated membrane permeabilization.

Jarva, M.Phan, T.K.Lay, F.T.Caria, S.Kvansakul, M.Hulett, M.D.

(2018) Sci Adv 4: eaat0979-eaat0979

  • DOI: https://doi.org/10.1126/sciadv.aat0979
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human defensins belong to a subfamily of the cationic antimicrobial peptides and act as a first line of defense against invading microbes. Their often broad-spectrum antimicrobial and antitumor activities make them attractive for therapeutic development; however, their precise molecular mechanism(s) of action remains to be defined. We show that human β-defensin 2 (HBD-2) permeabilizes Candida albicans cell membranes via a mechanism targeting the plasma membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP 2 ). We determined the structure of HBD-2 bound to PIP 2 , which revealed two distinct PIP 2 -binding sites, and showed, using functional assays, that mutations in these sites ablate PIP 2 -mediated fungal growth inhibition by HBD-2. Our study provides the first insight into lipid-mediated human defensin membrane permeabilization at an atomic level and reveals a unique mode of lipid engagement to permeabilize cell membranes.

  • Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-defensin 4A
A, B
41Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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
PIO (Subject of Investigation/LOI)
Query on PIO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
Binding Affinity Annotations 
IDSourceBinding Affinity
PIO Binding MOAD:  6CS9 IC50: 2200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.871α = 90
b = 25.538β = 98.64
c = 40.17γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaFT130101349

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description