SMTL ID : 5lxi.1

GABARAP-L1 ATG4B LIR Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

hetero-2-2-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.51, H.75 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.75, H2O.1, H2O.1, H2O.2, H2O.2 MG.7: 2 residues within 4Å: Chain B: R.73, H.75 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.75, H2O.3, H2O.3, H2O.3, H2O.4 MG.8: 2 residues within 4Å: Chain B: D.33, D.60 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.60, H2O.3, H2O.3, H2O.3, H2O.4

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 7 residues within 4Å: Chain A: Y.67, L.82, F.83, F.84, I.90, T.93 Ligands: PGE.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.84, A:F.84 Water bridges: A:T.93 PGE.3: 8 residues within 4Å: Chain A: V.63, Y.67, L.82, F.83, I.90, P.91, T.93 Ligands: PGE.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.91 Water bridges: A:T.93, A:T.93

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

EDO.4: 3 residues within 4Å: Chain A: Q.65, F.68, L.69 No protein-ligand interaction detected (PLIP)

2 x PER: PEROXIDE ION(Non-covalent)

PER.5: 5 residues within 4Å: Chain A: Y.31, P.32, D.33, R.34 Chain C: L.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.33, A:R.34, A:R.34 PER.6: 1 residues within 4Å: Chain A: R.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34, A:R.34

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 5 residues within 4Å: Chain B: Y.67, F.68, R.71, D.80, A.81 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skytte Rasmussen, M. et al., ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8. Autophagy (2017)

Release Date

2017-02-08

Peptides

Gamma-aminobutyric acid receptor-associated protein-like 1: AB
Cysteine protease ATG4B: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

C
C

D
E

Gamma-aminobutyric acid receptor-associated protein-like 1

Cysteine protease ATG4B

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