SMTL ID : 5jy0.1

Crystal structure of Porphyromonas endodontalis DPP11 in complex with substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x LEU- ASP- VAL: LEU-ASP-VAL(Non-covalent)

LEU-ASP-VAL.1: 17 residues within 4Å: Chain A: G.48, C.49, H.65, N.197, W.198, R.202, D.206, N.312, T.627, T.628, G.629, G.630, N.631, A.632, F.648, D.649, R.650 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.197, A:N.312, A:N.312, A:G.630, A:N.631, A:A.632, A:F.648, A:D.649 Salt bridges: A:R.650

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 7 residues within 4Å: Chain A: G.256, T.257, R.316, T.628, G.629, R.650, D.658 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.257, A:T.257, A:R.316, A:T.628, A:G.629, A:G.629, A:R.650 TRS.3: 7 residues within 4Å: Chain A: Q.241, G.242, V.243, K.575, N.612, S.613, R.674 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.243, A:K.575, A:S.613, A:S.613, A:R.674, A:R.674 Water bridges: A:D.614

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Asp/Glu-specific dipeptidyl-peptidase

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