SMTL ID : 6ikg.1

Crystal structure of substrate-bound S9 peptidase (S514A mutant) from Deinococcus radiodurans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

2 x MET- ALA- ALA: MET-ALA-ALA(Non-covalent)

MET-ALA-ALA.1: 10 residues within 4Å: Chain B: N.276, G.435, G.436, A.515, Y.516, R.538, F.556, R.600, H.630, R.634 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.556, B:F.556 Hydrogen bonds: B:G.436, B:G.436, B:Y.516, B:R.600, B:H.630 Salt bridges: B:R.538, B:H.630, B:R.634 MET-ALA-ALA.2: 11 residues within 4Å: Chain A: W.225, N.276, G.435, G.436, A.515, Y.516, R.538, F.556, R.600, H.630, R.634 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.556 Hydrogen bonds: A:G.436, A:G.436, A:Y.516, A:R.600, A:H.630 Salt bridges: A:R.538, A:H.630, A:R.634

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: Y.350, D.351, V.368, L.370, E.382, L.383, N.384, G.385 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.351, A:D.351, A:V.368, A:G.385 GOL.4: 8 residues within 4Å: Chain B: Y.350, D.351, V.368, L.370, E.382, L.383, N.384, G.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.351, B:V.368, B:G.385 GOL.5: 8 residues within 4Å: Chain B: A.375, L.419, G.444, F.445, T.446, F.449, Q.450, Y.461 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.446, B:T.446, B:Q.450 GOL.6: 8 residues within 4Å: Chain C: Y.350, D.351, V.368, L.370, E.382, L.383, N.384, G.385 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.351, C:D.351, C:E.382, C:G.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, P. et al., Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms. J.Biol.Chem. (2019)

Release Date

2018-11-14

Peptides

Acyl-peptide hydrolase, putative: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acyl-peptide hydrolase, putative

Related Entries With Identical Sequence