SMTL ID : 2aj8.3 (3 other biounits)

Porcine dipeptidyl peptidase IV (CD26) in complex with 7-Benzyl-1,3-dimethyl-8-piperazin-1-yl-3,7-dihydro-purine-2,6-dione (BDPX)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

7 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: 7 residues within 4Å: Chain A: T.150, I.156, Q.189, N.191, T.193, E.194, K.229 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: R.559, G.561, T.562, 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: 8 residues within 4Å: Chain B: R.559, G.561, T.562, M.600, 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 NAG-NAG.5: 9 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:R.559, C:R.559, C:E.566 NAG-NAG.7: 7 residues within 4Å: Chain D: T.150, I.156, Q.189, N.191, T.193, E.194, K.229 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain D: A.281, N.283, S.311, T.312, R.558, E.639, D.640 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.558, D:E.639, D:D.640 NAG-NAG.9: 9 residues within 4Å: Chain D: R.559, G.561, T.562, E.566, M.600, Y.644, N.647, S.648, R.653 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.559, D:E.566

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

NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: E.35, N.36, N.37, N.54 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain D: E.35, N.36, N.37, N.54 No protein-ligand interaction detected (PLIP)

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

NAG.10: 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.11: 4 residues within 4Å: Chain A: E.35, N.36, N.37, N.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:N.54 NAG.12: 3 residues within 4Å: Chain A: N.241 Chain C: Y.247, V.250 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.241 Water bridges: C:V.250 NAG.13: 6 residues within 4Å: Chain A: A.281, 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.17: 5 residues within 4Å: Chain B: L.40, N.42, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) NAG.18: 7 residues within 4Å: Chain B: T.150, I.156, Q.189, N.191, T.193, E.194, K.229 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.150, B:I.156 Hydrogen bonds: B:N.191, B:E.194, B:E.194 Water bridges: B:Q.189, B:K.229 NAG.19: 6 residues within 4Å: Chain B: P.240, N.241 Chain D: Y.247, V.250, L.256, R.298 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Water bridges: D:Y.247, D:R.298 Hydrophobic interactions: B:P.240 Hydrogen bonds: B:N.241 NAG.20: 4 residues within 4Å: Chain B: N.283, S.311, T.312, R.558 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.283, B:R.558 NAG.24: 4 residues within 4Å: Chain C: L.40, N.47, S.48, S.49 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.40 Hydrogen bonds: C:N.47 Water bridges: C:N.42 NAG.25: 4 residues within 4Å: Chain C: E.35, N.36, N.37, N.54 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.36, C:N.37, C:N.54 NAG.26: 7 residues within 4Å: Chain C: T.150, I.156, Q.189, N.191, T.193, E.194, K.229 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.150, C:I.156 Hydrogen bonds: C:N.191, C:T.193, C:E.194 Water bridges: C:T.227 NAG.27: 3 residues within 4Å: Chain A: Y.247, V.250 Chain C: N.241 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.241, A:Y.247 NAG.28: 5 residues within 4Å: Chain C: A.281, N.283, S.311, T.312, R.558 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.558 NAG.32: 4 residues within 4Å: Chain D: Y.45, N.47, S.48, S.49 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.47 NAG.33: 2 residues within 4Å: Chain B: V.250 Chain D: N.241 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.247

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

SO4.14: 6 residues within 4Å: Chain A: A.322, E.323, H.325, I.336, G.368, I.369 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.323, A:I.369 Water bridges: A:I.367, A:I.369 Salt bridges: A:H.325 SO4.21: 6 residues within 4Å: Chain B: A.322, E.323, H.325, I.336, G.368, I.369 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.323, B:I.369 Water bridges: B:I.367 Salt bridges: B:H.325 SO4.29: 6 residues within 4Å: Chain C: A.322, E.323, H.325, I.336, G.368, I.369 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.323, C:I.369 Water bridges: C:E.323 Salt bridges: C:H.325 SO4.34: 6 residues within 4Å: Chain D: A.322, E.323, H.325, I.336, G.368, I.369 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.323, D:I.369 Water bridges: D:E.323 Salt bridges: D:H.325

8 x SC3: 7-BENZYL-1,3-DIMETHYL-8-PIPERAZIN-1-YL-3,7-DIHYDRO-PURINE-2,6-DIONE(Non-covalent)

SC3.15: 10 residues within 4Å: Chain A: E.167, E.168, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628, V.673 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.593, A:V.618, A:Y.624, A:Y.624, A:V.673 Hydrogen bonds: A:R.87, A:E.167, A:Y.593 Water bridges: A:E.168, A:Y.509 pi-Stacking: A:Y.509, A:Y.628 SC3.16: 9 residues within 4Å: Chain A: W.149, N.241, A.242, S.243, V.244 Chain C: F.231, S.243, S.246 Ligands: SC3.31 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:V.244 pi-Stacking: A:W.149, A:W.149, A:W.149 Hydrophobic interactions: C:F.231 SC3.22: 10 residues within 4Å: Chain B: E.167, E.168, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628, V.673 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.593, B:V.618, B:Y.624, B:Y.624, B:V.673 Hydrogen bonds: B:R.87, B:E.167, B:Y.593 Water bridges: B:Y.509 pi-Stacking: B:Y.509, B:Y.628 SC3.23: 9 residues within 4Å: Chain B: W.149, N.241, A.242, S.243, V.244 Chain D: F.231, S.243, S.246 Ligands: SC3.36 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:V.244 pi-Stacking: B:W.149, B:W.149, B:W.149 Hydrophobic interactions: D:F.231 SC3.30: 10 residues within 4Å: Chain C: E.167, E.168, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628, V.673 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.593, C:V.618, C:Y.624, C:Y.624, C:V.673 Hydrogen bonds: C:E.167, C:E.168, C:Y.593 Water bridges: C:R.87 pi-Stacking: C:Y.509, C:Y.628 SC3.31: 8 residues within 4Å: Chain A: F.231, S.243, S.246 Chain C: W.149, A.242, S.243, V.244 Ligands: SC3.16 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:V.244 pi-Stacking: C:W.149, C:W.149, C:W.149 Hydrophobic interactions: A:F.231 SC3.35: 12 residues within 4Å: Chain D: R.87, E.167, E.168, Y.509, W.591, S.592, Y.593, V.618, W.621, Y.624, Y.628, V.673 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.593, D:V.618, D:W.621, D:Y.624, D:Y.624, D:V.673 Hydrogen bonds: D:R.87, D:E.167, D:E.167, D:Y.593 pi-Stacking: D:Y.509, D:Y.628 SC3.36: 9 residues within 4Å: Chain B: F.231, S.243, S.246 Chain D: W.149, N.241, A.242, S.243, V.244 Ligands: SC3.23 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:F.231 Hydrogen bonds: D:V.244 pi-Stacking: D:W.149, D:W.149, D:W.149

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dipeptidyl peptidase 4

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