SMTL ID : 5yp4.2 (1 other biounit)

Crystal structure of dipeptidyl peptidase IV (DPP IV) with Lys-Pro from Pseudoxanthomonas mexicana WO24

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 5 residues within 4Å: Chain A: E.209, A.531, Y.645, N.691 Ligands: PRO.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.531 Hydrogen bonds: A:Y.645, A:Y.645, A:N.691 LYS.10: 6 residues within 4Å: Chain B: R.106, E.208, E.209, Y.645, N.691 Ligands: PRO.11 6 PLIP interactions: 6 interactions with chain B, Hydrogen bonds: B:R.106, B:E.208, B:E.209, B:Y.645, B:N.691 Water bridges: B:D.211

2 x PRO: PROLINE(Non-covalent)(Covalent)

PRO.2: 7 residues within 4Å: Chain A: Y.527, S.613, N.614, W.642, Y.645, Y.649 Ligands: LYS.1 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:W.642, A:Y.649 Hydrogen bonds: A:Y.527, A:S.613, A:N.614, A:Y.645 Water bridges: A:S.613, A:S.613 PRO.11: 9 residues within 4Å: Chain B: Y.527, S.613, N.614, V.639, Y.645, Y.649, V.692, H.721 Ligands: LYS.10 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:V.639, B:Y.649, B:V.692 Hydrogen bonds: B:N.614

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.542, S.543, D.544, W.612, G.722, L.723, R.731 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.543, A:D.544, A:D.544, A:L.723, A:R.731, A:R.731 Water bridges: A:D.544, A:D.544, A:D.544, A:W.612, A:H.721 GOL.4: 4 residues within 4Å: Chain A: T.31, G.32, S.33, G.725 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.31, A:T.31, A:G.725 GOL.5: 5 residues within 4Å: Chain B: A.498, D.499, R.564, V.584, D.587 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.564, B:R.564, B:D.587 GOL.6: 5 residues within 4Å: Chain B: R.106, I.107, A.108, A.109, R.724 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.102, B:A.108, B:A.109 GOL.7: 6 residues within 4Å: Chain B: S.119, D.121, K.123, F.135, G.165, L.181 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.121, B:G.165 GOL.8: 7 residues within 4Å: Chain B: D.449, T.450, L.452, V.473, R.484, H.487, W.539 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.450 Water bridges: B:H.487 GOL.9: 5 residues within 4Å: Chain B: K.43, E.98, R.101, Q.105, D.115 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.43, B:K.43, B:E.98, B:R.101, B:R.101, B:Q.105 Water bridges: B:D.158

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
C

B
D

Dipeptidyl aminopeptidase 4

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