3L8L Antibiotic date Dec 31, 2009
title Gramicidin D Complex With Sodium Iodide
authors A.Olczak, M.L.Glowka, M.Szczesio, J.Bojarska, Z.Wawrzak, W.L.Duax
compound source
Molecule: Gramicidin D
Chain: A, C
Synonym: Val-Gramicidin A
 Organism_scientific: Bacillus Brevis
Organism_taxid: 1393

Molecule: Gramicidin D
Chain: B, D
Synonym: Val-Gramicidin A
Organism_scientific: Bacillus Brevis
Organism_taxid: 1393
symmetry Space Group: P 21 21 21
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
29.816 31.255 51.667 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.25 Å
ligand DLE, DVA, ETA, FVA, IOD, MOH, NA enzyme
Primary referenceThe first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex., Olczak A, Glowka ML, Szczesio M, Bojarska J, Wawrzak Z, Duax WL, Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):874-80. Epub 2010, Jul 9. PMID:20693686
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (34 Kb) [Save to disk]
  • Biological Unit Coordinates (3l8l.pdb1.gz) 15 Kb
  • Biological Unit Coordinates (3l8l.pdb2.gz) 14 Kb
  • LPC: Ligand-Protein Contacts for 3L8L
  • CSU: Contacts of Structural Units for 3L8L
  • Structure Factors (234 Kb)
  • Retrieve 3L8L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L8L from S2C, [Save to disk]
    • View 3L8L in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3L8L
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3L8L, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l8l_D] [3l8l_C] [3l8l_B] [3l8l_A] [3l8l]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3L8L
  • Community annotation for 3L8L at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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