5CGN

Structure of quasiracemic Ala-Magainin 2 with a beta amino acid substitution at position 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Quasiracemate Crystal Structures of Magainin 2 Derivatives Support the Functional Significance of the Phenylalanine Zipper Motif.

Hayouka, Z.Thomas, N.C.Mortenson, D.E.Satyshur, K.A.Weisblum, B.Forest, K.T.Gellman, S.H.

(2015) J.Am.Chem.Soc. 137: 11884-11887

  • DOI: 10.1021/jacs.5b07206
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Quasiracemic crystallography has been used to explore the significance of homochiral and heterochiral associations in a set of host-defense peptide derivatives. The previously reported racemic crystal structure of a magainin 2 derivative displayed a ...

    Quasiracemic crystallography has been used to explore the significance of homochiral and heterochiral associations in a set of host-defense peptide derivatives. The previously reported racemic crystal structure of a magainin 2 derivative displayed a homochiral antiparallel dimer association featuring a "phenylalanine zipper" notable for the dual roles of phenylalanines in mediating dimerization and formation of an exposed hydrophobic swath. This motif is seen as well in two new quasiracemate crystals that contain the d form of the magainin 2 derivative along with an l-peptide in which one Ala has been replaced by a β-amino acid residue. This structural trend supports the hypothesis that the Phe zipper motif has functional significance.


    Organizational Affiliation

    Department of Chemistry, ‡Department of Medicine, and §Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-Ala-Magainin Derivative
A, B, C, D
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
L-ACPC8-Ala-Magainin
E, F, G, H
23Xenopus laevisMutation(s): 0 
Gene Names: magainins
Find proteins for P11006 (Xenopus laevis)
Go to UniProtKB:  P11006
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  12 Unique
IDChainsTypeFormula2D DiagramParent
DIL
Query on DIL
A, B, C, D
D-PEPTIDE LINKINGC6 H13 N O2

--

DLY
Query on DLY
A, B, C, D
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DHI
Query on DHI
A, B, C, D
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DVA
Query on DVA
A, B, C, D
D-PEPTIDE LINKINGC5 H11 N O2

--

DLE
Query on DLE
A, B, C, D
D-PEPTIDE LINKINGC6 H13 N O2

--

DGL
Query on DGL
A, B, C, D
D-PEPTIDE LINKINGC5 H9 N O4

--

DAL
Query on DAL
A, B, C, D
D-PEPTIDE LINKINGC3 H7 N O2

--

DPN
Query on DPN
A, B, C, D
D-PEPTIDE LINKINGC9 H11 N O2

--

MED
Query on MED
A, B, C, D
D-PEPTIDE LINKINGC5 H11 N O2 S

--

DSE
Query on DSE
A, B, C, D
D-PEPTIDE LINKINGC4 H9 N O3

--

DSG
Query on DSG
A, B, C, D
D-PEPTIDE LINKINGC4 H8 N2 O3

--

XCP
Query on XCP
E, F, G, H
peptide-likeC6 H11 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 56.690α = 90.00
b = 56.690β = 90.00
c = 51.650γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM061238
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM08293
National Science Foundation (United States)United StatesNSF DMR-832760
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM100346

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references
  • Version 1.2: 2015-10-07
    Type: Derived calculations
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations