SMTL ID : 1tkr.1

Human Dipeptidyl Peptidase IV/CD26 inhibited with Diisopropyl FluoroPhosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NDG- FUC: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-FUC.1: 7 residues within 4Å: Chain A: E.29, V.40, N.42, Y.45, N.47, S.48, S.49 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.40 Hydrogen bonds: A:N.47 Water bridges: A:E.29, A:E.29, A:S.49, A:S.49, A:S.49

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 3 residues within 4Å: Chain A: R.109, I.110, N.112 No protein-ligand interaction detected (PLIP)

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.3: 8 residues within 4Å: Chain A: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:E.271, A:E.271, A:E.294 NAG-NAG.5: 3 residues within 4Å: Chain A: W.149, V.241, N.243 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: N.181, T.183, N.234, Q.270, E.271, E.294 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.234, B:Y.292

1 x NAG- NDG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-MAN.4: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194, A:E.194 Water bridges: A:Q.189

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.7: 5 residues within 4Å: Chain B: N.42, Y.45, N.47, S.48, S.49 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.42, B:N.47 Hydrogen bonds: B:N.42, B:S.49 Water bridges: B:N.47

2 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(Post Translational Modification)

NAG-NAG-BMA.9: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain B: W.149, T.150, N.243 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.150, B:T.150

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

NAG-NDG.11: 7 residues within 4Å: Chain B: I.281, N.283, M.310, S.311, T.312, R.558, D.640 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.312

2 x DFP: DIISOPROPYL PHOSPHONATE(Covalent)

DFP.12: 10 residues within 4Å: Chain A: R.87, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, V.673, H.702 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.593, A:V.618, A:W.621, A:Y.624, A:Y.628, A:Y.628 Hydrogen bonds: A:Y.593 Salt bridges: A:H.702 DFP.14: 9 residues within 4Å: Chain B: R.87, Y.509, S.592, Y.593, W.621, Y.624, Y.628, V.673, H.702 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.621, B:Y.624, B:Y.628, B:Y.628 Hydrogen bonds: B:Y.509, B:Y.593 Salt bridges: B:H.702

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

NAG.13: 2 residues within 4Å: Chain B: R.109, N.112 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:R.109, B:N.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bjelke, J.R. et al., Tyrosine 547 Constitutes an Essential Part of the Catalytic Mechanism of Dipeptidyl Peptidase IV. J.Biol.Chem. (2004)

Release Date

2004-07-06

Peptides

Dipeptidyl peptidase IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase IV

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