› 3l8l

X-ray diffraction
1.25Å resolution

Gramicidin D complex with sodium iodide

Released:
DOI: 10.2210/pdb3l8l/pdb
PDB entry 3l8l coloured by chain, front view.
PDB entry 3l8l coloured by chain, side view.
PDB entry 3l8l coloured by chain, top view.
Source organism: Brevibacillus brevis
Primary publication:
The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex.
Olczak A, Główka ML, Szczesio M, Bojarska J, Wawrzak Z, Duax WL
Acta Crystallogr D Biol Crystallogr 66 874-80 (2010)
PMID: 20693686

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163726 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
GRAMICIDIN D Chains: A, C
Molecule details ›
Chains: A, C
Length: 16 amino acids
Theoretical weight: 1.88 KDa
Source organism: Brevibacillus brevis
GRAMICIDIN D Chains: B, D
Molecule details ›
Chains: B, D
Length: 16 amino acids
Theoretical weight: 1.84 KDa
Source organism: Brevibacillus brevis

Ligands and Environments

3 bound ligands:
Ligand NA 4 x NA
Ligand IOD 7 x IOD
Ligand MOH 3 x MOH
3 modified residues:
Ligand FVA 4 x FVA
Ligand DLE 16 x DLE
Ligand DVA 8 x DVA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P212121
Unit cell:
a: 29.816Å b: 31.255Å c: 51.667Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 not available not available

Quick links

Citations

1 review citation

Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold.
Bojarska et al. (2021)
7 other articles

1 mention without citation

Membrane Protein Crystallization in Lipidic Mesophases. Hosting lipid affects on the crystallization and structure of a transmembrane peptide.
Höfer et al. (2011)