1AV2 | pdb_00001av2

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 (Depositor)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 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

PubMed: 9789021 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.95.22.12950
Primary Citation 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

Macromolecule Content

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

Macromolecules

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
CS Query on CS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain V [auth C] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth D] MOL2 format, chain V [auth C] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth D] mmCIF format, chain V [auth C] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B], V [auth C], W [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain V [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain V [auth C] Focus chain W [auth D]
MOH Query on MOH Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain X [auth D] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain X [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain X [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DLE Query on DLE	A, B, C, D	D-PEPTIDE LINKING	C₆ H₁₃ N O₂		--
DVA Query on DVA	A, B, C, D	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--
FVA Query on 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 Query on PRD_000150	A, B, C, D	GRAMICIDIN A	Polypeptide / Antibiotic		Interactions Focus chain A Focus chain B Focus chain C Focus chain D Interactions & Density Focus chain A Focus chain B Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.186 (Depositor)
R-Value Observed: 0.154 (Depositor)

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

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Entry History

Deposition Data

Released Date: 1998-07-01

Deposition Author(s):

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
Version 2.2: 2024-11-13
Changes: Structure summary