SMTL ID : 6jtb.1

Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from Porphyromonas gingivalis (Space)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: W.219, T.651, G.652, R.673 Ligands: CIT.2, CIT.4, K.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.651, A:G.652, A:R.673 Water bridges: A:N.333, A:N.333, A:G.653

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 11 residues within 4Å: Chain A: H.85, W.219, T.651, G.652, G.653, S.655, F.671, D.672, R.673 Ligands: PEG.1, K.9 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.653, A:S.655, A:S.655 Water bridges: A:N.333, A:N.654, A:N.670, A:F.671, A:D.672 Salt bridges: A:H.85, A:R.673 CIT.3: 2 residues within 4Å: Chain A: R.632 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.632 CIT.4: 7 residues within 4Å: Chain A: T.278, H.280, R.299, R.337, D.681 Ligands: PEG.1, K.10 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.278, A:R.337, A:R.337 Water bridges: A:H.280, A:H.280, A:W.291, A:R.299, A:R.299, A:R.299 Salt bridges: A:H.280, A:R.299, A:R.337, A:R.337

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: D.60, F.124, K.194, Y.196, P.253, K.254, R.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.60, A:K.194, A:K.254, A:R.255 GOL.6: 4 residues within 4Å: Chain A: D.297, I.298, R.301, M.396 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.297 GOL.7: 5 residues within 4Å: Chain A: R.632, A.634, D.635, R.636 Ligands: CIT.3 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.261, A:L.261, A:G.631, A:R.632 GOL.8: 5 residues within 4Å: Chain A: R.391, Y.394, Y.539, L.542, D.546 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.546 Water bridges: A:R.391

2 x K: POTASSIUM ION(Non-covalent)

K.9: 4 residues within 4Å: Chain A: N.218, W.219, D.672 Ligands: CIT.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.672, H2O.7 K.10: 5 residues within 4Å: Chain A: T.278, T.651, D.681 Ligands: PEG.1, CIT.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.278, A:T.651, A:D.681, H2O.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakamoto, Y. et al., Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase. Sci Rep (2019)

Release Date

2019-10-02

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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