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 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: 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 ...

    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   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GRAMICIDIN AA, B, C, D16Brevibacillus brevisMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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], T [auth C], U [auth C]CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
MOH
Query on MOH

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , K [auth A] , O [auth B] , P [auth B] , Q [auth B] , R [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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FVA
Query on FVA
A, B, C, DL-PEPTIDE LINKINGC6 H11 N O3VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000150
Query on PRD_000150
A, B, C, DGRAMICIDIN APolypeptide / Antibiotic Ligand Interaction
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

View Full Validation Report




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