SMTL ID : 5jwg.1

Crystal structure of Porphyromonas endodontalis DPP11 in complex with dipeptide Arg-Asp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ARG: ARGININE(Non-covalent)

ARG.1: 10 residues within 4Å: Chain A: H.65, S.193, N.197, W.198, A.308, Q.311, N.312, F.648, D.649 Ligands: ASP.2 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.193, A:N.197, A:N.197, A:A.308, A:N.312, D.2 Water bridges: A:R.316, R.1 ARG.5: 10 residues within 4Å: Chain B: H.65, S.193, N.197, W.198, A.308, Q.311, N.312, F.648, D.649 Ligands: ASP.6 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:S.193, B:N.197, B:N.197, B:A.308, B:N.312, D.6 Water bridges: B:R.316, R.5

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.2: 11 residues within 4Å: Chain A: H.65, W.198, T.628, G.629, G.630, N.631, A.632, F.648, D.649, R.650 Ligands: ARG.1 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.630, A:A.632, A:F.648, A:D.649, R.1, D.2 Water bridges: A:G.629, A:D.649 Salt bridges: A:H.65, A:R.650 ASP.6: 11 residues within 4Å: Chain B: H.65, W.198, T.628, G.629, G.630, N.631, A.632, F.648, D.649, R.650 Ligands: ARG.5 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:G.630, B:A.632, B:F.648, B:D.649, R.5 Water bridges: B:G.629 Salt bridges: B:H.65, B:R.650

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: E.339, A.342, W.343, M.540 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.343

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

NA.4: 4 residues within 4Å: Chain A: T.351, T.352, S.532, S.536 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.351, A:S.532

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

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