5INZ

Racemic structure of baboon theta defensin-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mirror Images of Antimicrobial Peptides Provide Reflections on Their Functions and Amyloidogenic Properties.

Wang, C.K.King, G.J.Conibear, A.C.Ramos, M.C.Chaousis, S.Henriques, S.T.Craik, D.J.

(2016) J Am Chem Soc 138: 5706-5713

  • DOI: https://doi.org/10.1021/jacs.6b02575
  • Primary Citation of Related Structures:  
    5INZ

  • PubMed Abstract: 

    Enantiomeric forms of BTD-2, PG-1, and PM-1 were synthesized to delineate the structure and function of these β-sheet antimicrobial peptides. Activity and lipid-binding assays confirm that these peptides act via a receptor-independent mechanism involving membrane interaction. The racemic crystal structure of BTD-2 solved at 1.45 Å revealed a novel oligomeric form of β-sheet antimicrobial peptides within the unit cell: an antiparallel trimer, which we suggest might be related to its membrane-active form. The BTD-2 oligomer extends into a larger supramolecular state that spans the crystal lattice, featuring a steric-zipper motif that is common in structures of amyloid-forming peptides. The supramolecular structure of BTD-2 thus represents a new mode of fibril-like assembly not previously observed for antimicrobial peptides, providing structural evidence linking antimicrobial and amyloid peptides.


  • Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Theta defensin-2, L-peptide
A, B, C
18Papio anubisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Theta defensin-2, D-peptide18synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
M [auth C]
N [auth C]
E [auth A],
F [auth A],
J [auth B],
M [auth C],
N [auth C],
O [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
K [auth B]
L [auth B]
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
P [auth C],
Q [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P -1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.248α = 100.67
b = 31.303β = 93.6
c = 37.926γ = 115.15
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP150100443
Australian Research Council (ARC)AustraliaAPP1026501
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1084965
National Health and Medical Research Council (NHMRC, Australia)Australia546578
Australian Research Council (ARC)AustraliaDE120103152

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description