SMTL ID : 4ka7.1

Structure of Organellar OligoPeptidase (E572Q) in complex with an endogenous substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ALA- ALA- ALA- ALA: short endogenous peptide substrate(Non-covalent)

ALA-ALA-ALA-ALA.1: 12 residues within 4Å: Chain A: A.443, W.444, M.445, H.494, Q.495, H.498, W.520, E.524, H.626, Y.632, Y.639 Ligands: ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.632 Hydrogen bonds: A:M.445, A:M.445, A:Q.495, A:Y.632, A:Y.632 Water bridges: A:G.631

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.494, H.498, E.524, S.527 Ligands: ALA-ALA-ALA-ALA.1, ALA-ALA-ALA-ALA.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.494, A:H.498, A:E.524, A:E.524

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: P.400, A.401, D.402, L.404, R.416 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.400, A:R.416 GOL.4: 6 residues within 4Å: Chain A: D.28, F.29, Y.427, R.463, L.464, V.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.28, A:L.464, A:L.464 Water bridges: A:Y.427 GOL.5: 5 residues within 4Å: Chain A: L.315, W.641, V.644, L.645, P.696 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.641

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: M.302, K.305, A.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.305, A:M.306

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 3 residues within 4Å: Chain A: Q.119, K.121, R.166 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kmiec, B. et al., Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts. Proc. Natl. Acad. Sci. U.S.A. (2013)

Release Date

2013-09-18

Peptides

Oligopeptidase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oligopeptidase A