4GDK Protein Binding date Jul 31, 2012
title Crystal Structure Of Human Atg12~Atg5 Conjugate In Complex W Terminal Fragment Of Atg16l1
authors C.Otomo, Z.Metlagel, G.Takaesu, T.Otomo
compound source
Molecule: Ubiquitin-Like Protein Atg12
Chain: A, D
Synonym: Autophagy-Related Protein 12, Apg12-Like
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apg12, Apg12l, Atg12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacyc Duet-1

Molecule: Autophagy Protein 5
Chain: B, E
Synonym: Apg5-Like, Apoptosis-Specific Protein
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apg5l, Asp, Atg5
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacyc Duet-1

Molecule: Autophagy-Related Protein 16-1
Chain: C, F
Synonym: Apg16-Like 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apg16l, Atg16l1, Unq9393pro34307
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 21 21 21
R_factor 0.176 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.757 113.153 210.685 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4GDK, from MSDmotif at EBI
  • Fold representative 4gdk from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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