1AV2

Gramicidin A/CsCl complex, active as a dimer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.186 
  • R-Value Observed: 0.154 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

The Conducting Form of Gramicidin a is a Right-Handed Double-Stranded Double Helix.

Burkhart, B.M., Li, N., Langs, D.A., Pangborn, W.A., Duax, W.L.

(1998) Proc Natl Acad Sci U S A 95: 12950

  • DOI: https://doi.org/10.1073/pnas.95.22.12950
  • Primary Citation of Related Structures:  
    1AV2, 1BDW

  • PubMed Abstract: 

    The linear pentadecapeptide antibiotic, gramicidin D, is a naturally occurring product of Bacillus brevis known to form ion channels in synthetic and natural membranes. The x-ray crystal structures of the right-handed double-stranded double-helical dimers (DSDH) reported here agree with 15N-NMR and CD data on the functional gramicidin D channel in lipid bilayers. These structures demonstrate single-file ion transfer through the channels. The results also indicate that previous crystal structure reports of a left-handed double-stranded double-helical dimer in complex with Cs+ and K+ salts may be in error and that our evidence points to the DSDH as the major conformer responsible for ion transport in membranes.

    • Organizational Affiliation: 

    Hauptman-Woodward Medical Research Institute, Inc., 73 High Street, Buffalo, NY 14203, USA. burkhart@hwi.buffalo.edu


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GRAMICIDIN A
A, B, C, D
16Brevibacillus brevisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CS
Query on CS
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
L [auth B]
M [auth B]
S [auth C]
E [auth A],
F [auth A],
L [auth B],
M [auth B],
S [auth C],
T [auth C],
U [auth C]
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
V [auth C],
W [auth D]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MOH
Query on MOH
Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
O [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
X [auth D]
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FVA
Query on FVA
A, B, C, D
L-PEPTIDE LINKINGC6 H11 N O3VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.186 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.06α = 90
b = 31.88β = 90
c = 52.11γ = 90
Software Package:
Software NamePurpose
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-07-01
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2013-02-06
    Changes: Derived calculations
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other
  • Version 2.1: 2024-04-03
    Changes: Refinement description