4GDK Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 date
authors Otomo, C., Metlagel, Z., Takaesu, G., Otomo, T.
compound source
symmetry
R_factor
R_Free 0.2361
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.70
ligand NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


Primary referenceStructure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy., Otomo C, Metlagel Z, Takaesu G, Otomo T, Nat Struct Mol Biol. 2012 Dec 2. doi: 10.1038/nsmb.2431. PMID:23202584
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (284 Kb) [Save to disk]
  • Biological Unit Coordinates (4gdk.pdb1.gz) 274 Kb
  • LPC: Ligand-Protein Contacts for 4GDK
  • CSU: Contacts of Structural Units for 4GDK
  • Structure Factors (167 Kb)
  • Retrieve 4GDK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GDK from S2C, [Save to disk]
  • Re-refined 4gdk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GDK 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 4GDK
  • 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 4GDK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gdk_F] [4gdk_B] [4gdk] [4gdk_D] [4gdk_E] [4gdk_A] [4gdk_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4GDK
  • Community annotation for 4GDK at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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