4GDK

Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1

Structural Biology Knowledgebase: 4GDK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.176

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GDK

Classification: PROTEIN BINDING

Total Structure Weight: 94904.20

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquitin-like protein ATG12 A, D 91 Homo sapiens Gene Name(s): ATG12 Gene View APG12 APG12L
Autophagy protein 5 B, E 275 Homo sapiens Gene Name(s): ATG5 Gene View APG5L ASP
Autophagy-related protein 16-1 C, F 36 Homo sapiens Gene Name(s): ATG16L1 Gene View APG16L UNQ9393/PRO34307

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NA
Query on NA

B, E SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.176
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.76 α = 90.00
b = 113.15 β = 90.00
c = 210.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-31
  • Released Date: 2012-12-05
  • Deposition author(s): Otomo, C., Metlagel, Z., Takaesu, G., Otomo, T.

Revision History

  • 2013-01-16
    Type: Citation | Details: Citation update
  • 2013-01-02
    Type: Citation | Details: Citation update