SMTL ID : 2ajd.2 (2 other biounits)

Porcine dipeptidyl peptidase IV (CD26) in complex with L-Pro-boro-L-Pro (boroPro)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-dimer

Ligands

4 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: 8 residues within 4Å: Chain A: R.559, G.561, T.562, E.566, M.600, Y.644, N.647, R.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.559, A:R.559 NAG-NAG.3: 5 residues within 4Å: Chain B: I.156, N.191, T.193, E.194, K.229 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain B: A.281, N.283, S.311, T.312, R.558, E.639, D.640 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.558, B:E.639, B:D.640 NAG-NAG.5: 7 residues within 4Å: Chain B: R.559, G.561, T.562, E.566, Y.644, N.647, R.653 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.566

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.2: 4 residues within 4Å: Chain B: E.35, N.36, N.37, N.54 No protein-ligand interaction detected (PLIP)

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

NAG.6: 5 residues within 4Å: Chain A: L.40, Y.45, 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.35, A:N.36, A:N.37, A:N.54, A:N.54 NAG.8: 7 residues within 4Å: Chain A: T.150, I.156, Q.189, N.191, T.193, E.194, K.229 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.150, A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194 NAG.9: 1 residues within 4Å: Chain A: N.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.10: 5 residues within 4Å: Chain A: A.281, N.283, S.311, R.558, D.640 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.283, A:R.558, A:D.640 NAG.13: 2 residues within 4Å: Chain B: N.47, S.49 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.47 NAG.14: 1 residues within 4Å: Chain B: N.241 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.241 Water bridges: B:N.241, B:N.241

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

SO4.11: 5 residues within 4Å: Chain A: A.322, E.323, H.325, G.368, I.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.323, A:E.323, A:I.369 Salt bridges: A:H.325 SO4.15: 7 residues within 4Å: Chain B: A.322, E.323, H.325, I.336, I.367, 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

2 x BPR: (2R)-N-[(2R)-2-(DIHYDROXYBORYL)-1-L-PROLYLPYRROLIDIN-2-YL]-N-[(5R)-5-(DIHYDROXYBORYL)-1-L-PROLYLPYRROLIDIN-2-YL]-L-PROLINAMIDE(Covalent)

BPR.12: 12 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, V.673, H.702 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.618, A:Y.628, A:V.673 Hydrogen bonds: A:R.87, A:R.87, A:E.167, A:E.167, A:Y.509, A:Y.509, A:Y.593, A:Y.624, A:N.672 BPR.16: 12 residues within 4Å: Chain B: R.87, E.167, E.168, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.618, B:Y.628, B:V.673 Hydrogen bonds: B:R.87, B:E.167, B:E.167, B:Y.509, B:Y.509, B:Y.593, B:Y.624, B:N.672

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
C

B
D

Dipeptidyl peptidase 4

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