6HOG

Structure of VPS34 LIR motif bound to GABARAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs.

Birgisdottir, A.B.Mouilleron, S.Bhujabal, Z.Wirth, M.Sjottem, E.Evjen, G.Zhang, W.Lee, R.O'Reilly, N.Tooze, S.A.Lamark, T.Johansen, T.

(2019) Autophagy --: 1-23


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
A
129Homo sapiensMutation(s): 0 
Gene Names: GABARAP (FLC3B), PIK3C3 (VPS34)
EC: 2.7.1.137
Find proteins for O95166 (Homo sapiens)
Go to Gene View: GABARAP
Go to UniProtKB:  O95166
Find proteins for Q8NEB9 (Homo sapiens)
Go to Gene View: PIK3C3
Go to UniProtKB:  Q8NEB9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.154 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 92.100α = 90.00
b = 92.100β = 90.00
c = 41.230γ = 120.00
Software Package:
Software NamePurpose
xia2data reduction
PHENIXrefinement
PHASERphasing
DIALSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway214448
Research Council of NorwayNorway249884

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references