2XDC Structure of linear gramicidin D obtained using Type I crystals grown in a lipid cubic phase. date
authors Hoefer, N., Aragao, D., Caffrey, M.
compound source
symmetry
R_factor
R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.70
ligand 15P, DLE, DVA, ETA, FVA, NA enzyme
Primary referenceCrystallizing transmembrane peptides in lipidic mesophases., Hofer N, Aragao D, Caffrey M, Biophys J. 2010 Aug 4;99(3):L23-5. PMID:20682243
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (2xdc.pdb1.gz) 10 Kb
  • Biological Unit Coordinates (2xdc.pdb2.gz) 7 Kb
  • Biological Unit Coordinates (2xdc.pdb3.gz) 8 Kb
  • LPC: Ligand-Protein Contacts for 2XDC
  • CSU: Contacts of Structural Units for 2XDC
  • Structure Factors (152 Kb)
  • Retrieve 2XDC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XDC from S2C, [Save to disk]
  • Re-refined 2xdc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XDC in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2XDC
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2XDC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xdc_F] [2xdc_D] [2xdc_B] [2xdc_A] [2xdc_C] [2xdc_E] [2xdc]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2XDC
  • Community annotation for 2XDC 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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