SMTL ID : 2ajb.1 (3 other biounits)

Porcine dipeptidyl peptidase IV (CD26) in complex with the tripeptide tert-butyl-Gly-L-Pro-L-Ile (tBu-GPI)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 9 residues within 4Å: Chain A: R.559, G.561, T.562, E.566, M.600, Y.644, N.647, S.648, R.653 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.559, A:R.559, A:Y.644 NAG-NAG.4: 7 residues within 4Å: Chain B: R.559, G.561, T.562, Y.644, N.647, S.648, R.653 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.559, B:R.559, B:Y.644

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: E.35, N.36, N.37, N.54 No protein-ligand interaction detected (PLIP)

2 x 0QG: 3-methyl-L-valyl-L-prolyl-L-isoleucine(Covalent)

0QG.5: 11 residues within 4Å: Chain A: R.87, E.167, E.168, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, H.702 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.509, A:Y.593, A:V.618, A:Y.628 Hydrogen bonds: A:R.87, A:E.167, A:Y.509, A:S.592, A:Y.593, A:N.672 Salt bridges: A:R.87, A:H.702 0QG.11: 13 residues within 4Å: Chain B: R.87, E.167, E.168, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.509, B:V.618, B:Y.628, B:V.673 Hydrogen bonds: B:R.87, B:E.167, B:S.592, B:Y.593, B:Y.624, B:N.672, B:H.702 Salt bridges: B:R.87, B:H.702

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 5 residues within 4Å: Chain A: L.40, N.42, N.47, S.48, S.49 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.40 Hydrogen bonds: A:N.47 NAG.7: 4 residues within 4Å: Chain A: E.35, N.36, N.37, N.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.37 NAG.8: 1 residues within 4Å: Chain A: N.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.9: 5 residues within 4Å: Chain A: N.283, I.310, S.311, T.312, D.640 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.310 Hydrogen bonds: A:N.283, A:D.640 NAG.12: 4 residues within 4Å: Chain B: L.40, N.47, S.48, S.49 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.47 NAG.13: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.156 Hydrogen bonds: B:N.191, B:E.194, B:E.194 Water bridges: B:K.229 NAG.14: 2 residues within 4Å: Chain B: P.240, N.241 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.240 Hydrogen bonds: B:N.241 NAG.15: 5 residues within 4Å: Chain B: N.283, I.310, S.311, T.312, R.558 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.310, B:T.312 Hydrogen bonds: B:N.283 Water bridges: B:N.283, B:R.558

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 7 residues within 4Å: Chain A: A.322, E.323, H.325, I.336, I.367, G.368, I.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.323, A:I.369 Water bridges: A:I.369 Salt bridges: A:H.325 SO4.16: 6 residues within 4Å: Chain B: A.322, E.323, H.325, I.336, G.368, I.369 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.323, B:I.369 Salt bridges: B:H.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engel, M. et al., Rigidity and flexibility of dipeptidyl peptidase IV: crystal structures of and docking experiments with DPIV. J.Mol.Biol. (2006)

Release Date

2006-02-28

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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