SMTL ID : 5jwf.1

Crystal structure of Porphyromonas gingivalis DPP11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain B: D.277, R.281, R.372, M.376, E.447 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.277, B:D.277, B:R.372 Water bridges: B:D.277 GOL.2: 6 residues within 4Å: Chain B: F.104, D.106, K.174, Y.176, P.233, K.234 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.106, B:K.234, B:R.235 GOL.3: 4 residues within 4Å: Chain B: N.198, W.199, F.651, D.652 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.198, B:W.199, B:F.651

1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.4: 3 residues within 4Å: Chain B: R.371, Y.374, L.522 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.522

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bezerra, G.A. et al., Bacterial protease uses distinct thermodynamic signatures for substrate recognition. Sci Rep (2017)

Release Date

2017-06-14

Peptides

Asp/Glu-specific dipeptidyl-peptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Asp/Glu-specific dipeptidyl-peptidase