SMTL ID : 5jxf.1 (3 other biounits)

Crystal structure of Flavobacterium psychrophilum DPP11 in complex with dipeptide Arg-Asp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x ARG: ARGININE(Non-covalent)

ARG.1: 9 residues within 4Å: Chain A: H.101, D.225, N.228, W.229, A.339, N.343, F.678, D.679 Ligands: ASP.2 6 PLIP interactions: 6 interactions with chain A, Hydrogen bonds: A:S.224, A:N.228, A:A.339, A:N.343, A:D.679 Salt bridges: A:D.225

1 x ASP: ASPARTIC ACID(Non-covalent)

ASP.2: 12 residues within 4Å: Chain A: H.101, W.229, T.657, T.658, G.659, G.660, N.661, S.662, F.678, D.679, R.680 Ligands: ARG.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.657, A:T.657, A:G.660, A:N.661, A:S.662, A:F.678, A:D.679 Salt bridges: A:R.680

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain B: Y.638, G.642, G.645 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain B: T.657, T.658, N.677, D.679, R.680 Ligand excluded by PLIP

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

NA.5: 4 residues within 4Å: Chain B: E.276, G.594, Y.602, P.605 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.276, B:G.594, B:Y.602

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
D

Asp/Glu-specific dipeptidyl-peptidase

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