5CGO | pdb_00005cgo

Structure of quasiracemic Ala-Magainin 2 with a beta amino acid substitution at position 13

• PDB DOI: https://doi.org/10.2210/pdb5CGO/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2015-07-09 Released: 2015-09-23 
• Deposition Author(s): Hayouka, Z., Thomas, N.C., Mortenson, D.E., Satyshur, K.A., Weisblum, B., Forest, K.T., Gellman, S.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

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

• PubMed: 26369301 
• DOI: https://doi.org/10.1021/jacs.5b07206
• Primary Citation Related Structures: 
  5CGN, 5CGO


• 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 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crystals that contain the d form of the magainin 2 derivative along with an l-peptide in which one Ala has been replaced by a β-amino acid residue.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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.04 kDa 
• Atom Count: 750 
• Modeled Residue Count: 92 
• Deposited Residue Count: 92 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACPC-13 derivative of Ala-Magainin 2	A, B	23	synthetic construct	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P11006 (Xenopus laevis) Explore P11006  Go to UniProtKB:  P11006

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-Ala-Magainin 2	C, D	23	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  12 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
XCP	A, B	PEPTIDE-LIKE	C6 H11 N O2		--
DAL	C, D	D-PEPTIDE LINKING	C3 H7 N O2		--
DGL	C, D	D-PEPTIDE LINKING	C5 H9 N O4		--
DHI	C, D	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DIL	C, D	D-PEPTIDE LINKING	C6 H13 N O2		--
DLE	C, D	D-PEPTIDE LINKING	C6 H13 N O2		--
DLY	C, D	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DPN	C, D	D-PEPTIDE LINKING	C9 H11 N O2		--
DSE	C, D	D-PEPTIDE LINKING	C4 H9 N O3		--
DSG	C, D	D-PEPTIDE LINKING	C4 H8 N2 O3		--
DVA	C, D	D-PEPTIDE LINKING	C5 H11 N O2		--
MED	C, D	D-PEPTIDE LINKING	C5 H11 N O2 S		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.85	α = 109.76
b = 27	β = 102.35
c = 29.96	γ = 90.23

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Hayouka, Z., Thomas, N.C., Mortenson, D.E., Satyshur, K.A., Weisblum, B., Forest, K.T., Gellman, S.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM061238

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Database references
• Version 1.2: 2015-10-07
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2023-11-15
  Changes: Data collection, Derived calculations