SMTL ID : 8t33.1

Crystal structure of K46 acetylated GABARAP in complex with the LIR of TP53INP2/DOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: E.99, H.100 Ligands: ZN.6, ZN.7, ACT.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.99, ACT.10 ZN.2: 1 residues within 4Å: Chain A: E.103 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.103, H2O.1, H2O.5 ZN.3: 1 residues within 4Å: Chain A: H.101 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.101 ZN.4: 1 residues within 4Å: Chain A: H.11 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.11, H2O.5 ZN.5: 1 residues within 4Å: Chain A: D.56 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, H2O.3, H2O.6 ZN.6: 4 residues within 4Å: Chain A: E.99, H.100 Ligands: ZN.1, ACT.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.99, A:H.100 ZN.7: 6 residues within 4Å: Chain A: P.88, A.91, Q.95, E.99 Ligands: ZN.1, ACT.10 No protein-ligand interaction detected (PLIP) ZN.8: 1 residues within 4Å: Chain A: E.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.10, A:E.10, H2O.4 ZN.9: 1 residues within 4Å: Chain A: H.71 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.71, H2O.4, H2O.5

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 11 residues within 4Å: Chain A: V.82, V.85, I.86, P.87, P.88, L.96, E.99, H.100 Ligands: ZN.1, ZN.6, ZN.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.82, A:V.85, A:P.87, A:L.96 Salt bridges: A:H.100 ACT.11: 3 residues within 4Å: Chain A: R.17, E.21, K.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.21 Water bridges: A:R.17 Salt bridges: A:R.17, A:K.25 ACT.12: 2 residues within 4Å: Chain A: E.102, E.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.102, A:E.102, A:E.103 ACT.13: 4 residues within 4Å: Chain A: Y.63, L.78, F.79, T.89 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.63, A:T.89 Hydrogen bonds: A:Y.63 Water bridges: A:L.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ali, M.G. et al., Structural and functional characterization of the role of acetylation on the interactions of the human Atg8-family proteins with the autophagy receptor TP53INP2/DOR. Autophagy (2024)

Release Date

2024-05-22

Peptides

Gamma-aminobutyric acid receptor-associated protein: A
Tumor protein p53-inducible nuclear protein 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gamma-aminobutyric acid receptor-associated protein

Tumor protein p53-inducible nuclear protein 2

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