SMTL ID : 5yzo.1

Crystal structure of S9 peptidase mutant (S514A) from Deinococcus radiodurans R1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 7 residues within 4Å: Chain A: G.435, G.436, G.514, A.515, R.538, H.630, R.634 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.538, A:R.634, A:R.634 DMS.2: 3 residues within 4Å: Chain A: V.311, G.312, S.635 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.312 DMS.3: 5 residues within 4Å: Chain A: T.120, H.121, F.122, W.180, L.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.121 pi-Cation interactions: A:F.122 DMS.6: 7 residues within 4Å: Chain B: G.435, G.436, G.514, A.515, R.538, H.630, R.634 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.538, B:R.634, B:R.634 DMS.7: 4 residues within 4Å: Chain B: V.311, G.312, A.313, S.635 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.312 DMS.10: 7 residues within 4Å: Chain C: G.435, G.436, G.514, A.515, R.538, H.630, R.634 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.538, C:R.634, C:R.634 DMS.11: 3 residues within 4Å: Chain C: V.311, G.312, S.635 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.312, C:S.635 DMS.14: 7 residues within 4Å: Chain D: G.435, G.436, G.514, A.515, R.538, H.630, R.634 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.538, D:R.634, D:R.634 DMS.15: 3 residues within 4Å: Chain D: V.311, G.312, S.635 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.312, D:S.635

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: P.162, V.163, Y.164, R.165, G.548, T.549, S.550, D.551, L.554 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.164, A:R.165, A:G.548 Water bridges: A:Y.164, A:S.550, A:G.553, A:L.554 GOL.5: 6 residues within 4Å: Chain A: T.529, F.531, Q.532, K.587, T.588, P.589 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.532 Water bridges: A:T.528, A:K.587 GOL.8: 6 residues within 4Å: Chain B: T.529, F.531, Q.532, K.587, T.588, P.589 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.528, B:T.588 GOL.9: 6 residues within 4Å: Chain B: Y.441, T.446, E.448, F.449, R.538, R.644 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.441, B:R.538, B:R.538, B:R.644 Water bridges: B:G.307, B:T.446, B:G.514 GOL.12: 6 residues within 4Å: Chain C: T.529, F.531, Q.532, K.587, T.588, P.589 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.529, C:Q.532 Water bridges: C:K.587 GOL.13: 6 residues within 4Å: Chain C: Y.441, T.446, E.448, F.449, R.538, R.644 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.441, C:R.538, C:R.538, C:R.644 Water bridges: C:G.307, C:D.308, C:G.514, C:R.634

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

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