1AV2

Gramicidin A/CsCl complex, active as a dimer

• PDB DOI:  https://doi.org/10.2210/pdb1AV2/pdb

• Classification: ANTIBIOTIC
• Organism(s): Brevibacillus brevis
• Mutation(s): No 


• Deposited: 1997-09-23 Released: 1998-07-01 
• Deposition Author(s): Burkhart, B.M., Li, N., Langs, D.A., Duax, W.L.

---

Experimental Data Snapshot

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

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

• PubMed: 9789021 
• 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. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.89 kDa 
• Atom Count: 603 
• Modelled Residue Count: 64 
• Deposited Residue Count: 64 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GRAMICIDIN A	A, B, C, D	16	Brevibacillus brevis	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CS	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	G [auth A], N [auth B], V [auth C], W [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MOH	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
ID	Chains	Type	Formula	2D Diagram	Parent
FVA	A, B, C, D	L-PEPTIDE LINKING	C6 H11 N O3		VAL

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000150	A, B, C, D	GRAMICIDIN A	Polypeptide / 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 = 31.06	α = 90
b = 31.88	β = 90
c = 52.11	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXL-97	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-07-01 
Deposition Author(s): Burkhart, B.M., Li, N., Langs, D.A., Duax, W.L.

Revision History  

• 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