4NAW

Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3

Structural Biology Knowledgebase: 4NAW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.171

Literature

Macromolecules
Sequence Display for 4NAW

Classification: PROTEIN TRANSPORT / LIGASE

Total Structure Weight: 206156.41

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquitin-like protein ATG12 A, E, I, M 91 Homo sapiens Fragment: UNP residues 52-140
Gene Name(s): ATG12 Gene View APG12 APG12L
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Autophagy protein 5 B, F, J, N 275 Homo sapiens Gene Name(s): ATG5 Gene View APG5L ASP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Autophagy-related protein 16-1 C, G, K, O 36 Homo sapiens Fragment: UNP residues 11-43
Gene Name(s): ATG16L1 Gene View APG16L UNQ9393/PRO34307
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquitin-like-conjugating enzyme ATG3 D, H, L, P 34 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: UNP residues 140-170
Gene Name(s): ATG3 Gene View APG3 APG3L
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

B, F, J, N SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.171
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 93.58 α = 90.00
b = 120.10 β = 90.00
c = 189.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-22
  • Released Date: 2013-11-06
  • Deposition author(s): Metlagel, Z., Otomo, C., Takaesu, G., Otomo, T.

Revision History

  • 2013-12-18
    Type: Citation | Details: Citation update
  • 2013-11-27
    Type: Citation | Details: Citation update