SMTL ID : 5yp2.1

Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x 8YC: (2S,5R)-1-[2-[[1-(hydroxymethyl)cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile(Covalent)

8YC.1: 14 residues within 4Å: Chain A: R.106, E.208, E.209, Y.527, A.531, S.613, N.614, V.639, W.642, Y.645, Y.649, N.691, V.692, H.721 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.531, A:V.639, A:W.642, A:Y.645, A:V.692 Hydrogen bonds: A:R.106, A:E.208, A:Y.527, A:S.613, A:N.614, A:Y.645, A:N.691 Water bridges: A:Y.649 8YC.4: 13 residues within 4Å: Chain B: R.106, E.208, E.209, Y.527, A.531, S.613, N.614, V.639, Y.645, Y.649, N.691, V.692, H.721 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.531, B:V.639, B:Y.645, B:V.692 Hydrogen bonds: B:R.106, B:E.208, B:Y.527, B:Y.527, B:N.614, B:N.691

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.106, I.107, A.108, A.109, R.724 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.109, A:R.724 Water bridges: A:G.722 GOL.3: 7 residues within 4Å: Chain A: S.543, D.544, W.612, H.721, G.722, L.723, R.731 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.543, A:L.723, A:R.731 GOL.5: 4 residues within 4Å: Chain B: R.106, I.107, A.108, A.109 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.108, B:A.109 Water bridges: B:E.103, B:E.103, B:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roppongi, S. et al., Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues. Sci Rep (2018)

Release Date

2018-02-21

Peptides

Dipeptidyl aminopeptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl aminopeptidase 4

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