SMTL ID : 6hog.1

Structure of VPS34 LIR motif bound to GABARAP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

homo-trimer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: T.104 Chain B: T.104 Chain C: T.104 Ligands: SO4.7, SO4.13 10 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:T.104, A:T.104, A:T.104, B:T.104 Water bridges: C:T.104, C:T.104, A:T.104, A:T.104, B:T.104, B:T.104 SO4.2: 4 residues within 4Å: Chain A: K.52, P.54, K.55, A.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55 Salt bridges: A:K.52 SO4.7: 5 residues within 4Å: Chain A: T.104 Chain B: T.104 Chain C: T.104 Ligands: SO4.1, SO4.13 10 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: C:T.104, A:T.104, B:T.104, B:T.104 Water bridges: C:T.104, C:T.104, A:T.104, A:T.104, B:T.104, B:T.104 SO4.8: 4 residues within 4Å: Chain B: K.52, P.54, K.55, A.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.55 Salt bridges: B:K.52 SO4.13: 5 residues within 4Å: Chain A: T.104 Chain B: T.104 Chain C: T.104 Ligands: SO4.1, SO4.7 10 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:T.104, C:T.104, A:T.104, B:T.104 Water bridges: C:T.104, C:T.104, A:T.104, A:T.104, B:T.104, B:T.104 SO4.14: 4 residues within 4Å: Chain C: K.52, P.54, K.55, A.56 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.55 Salt bridges: C:K.52

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: R.39, Y.112, H.116, F.120 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.39, A:H.116 EDO.4: 2 residues within 4Å: Chain A: K.19, K.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.19, A:K.23, A:K.23 Water bridges: A:R.31 EDO.9: 5 residues within 4Å: Chain B: R.39, Y.112, H.116, F.120 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.39, B:H.116 EDO.10: 2 residues within 4Å: Chain B: K.19, K.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.19, B:K.23, B:K.23 Water bridges: B:R.31 EDO.15: 5 residues within 4Å: Chain C: R.39, Y.112, H.116, F.120 Ligands: GOL.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.39, C:H.116 EDO.16: 2 residues within 4Å: Chain C: K.19, K.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.19, C:K.23, C:K.23 Water bridges: C:R.31

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: R.39, P.43, V.46, S.70, G.109, Y.112, Q.113 Ligands: EDO.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.39, A:R.39, A:P.43, A:S.70, A:Q.113 GOL.6: 3 residues within 4Å: Chain A: N.98, E.114, H.115 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.98, A:H.115 Water bridges: A:H.115, A:H.116 GOL.11: 8 residues within 4Å: Chain B: R.39, P.43, V.46, S.70, G.109, Y.112, Q.113 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.39, B:R.39, B:P.43, B:S.70, B:Q.113 GOL.12: 3 residues within 4Å: Chain B: N.98, E.114, H.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.98, B:H.115 Water bridges: B:H.115, B:H.116 GOL.17: 8 residues within 4Å: Chain C: R.39, P.43, V.46, S.70, G.109, Y.112, Q.113 Ligands: EDO.15 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.39, C:R.39, C:P.43, C:S.70, C:Q.113 GOL.18: 3 residues within 4Å: Chain C: N.98, E.114, H.115 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.98, C:H.115 Water bridges: C:H.115, C:H.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Birgisdottir, A.B. et al., Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs. Autophagy (2019)

Release Date

2019-02-27

Peptides

Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein