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

Porcine dipeptidyl peptidase IV (CD26) in complex with 4-(2-Aminoethyl)-benzene sulphonyl fluoride (AEBSF)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 6 residues within 4Å: Chain A: 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: 9 residues within 4Å: Chain B: 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 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: 6 residues within 4Å: Chain D: I.156, Q.189, N.191, T.193, E.194, K.229 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain D: 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 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.559

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: 2 residues within 4Å: Chain A: N.241 Chain C: Y.247 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:Y.247, C:Y.247, C:V.250 Hydrogen bonds: A:N.241 NAG.13: 5 residues within 4Å: Chain A: A.281, N.283, S.311, T.312, D.640 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.283, A:D.640 NAG.16: 4 residues within 4Å: Chain B: N.42, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) NAG.17: 6 residues within 4Å: Chain B: I.156, Q.189, N.191, T.193, E.194, K.229 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.156 Hydrogen bonds: B:N.191, B:E.194, B:E.194 Water bridges: B:Q.189, B:K.229 NAG.18: 4 residues within 4Å: Chain B: P.240, N.241 Chain D: Y.247, V.250 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:P.240 Hydrogen bonds: B:N.241 Water bridges: D:Q.248 NAG.19: 3 residues within 4Å: Chain B: N.283, S.311, T.312 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.312 Hydrogen bonds: B:N.283 Water bridges: B:N.283 NAG.22: 6 residues within 4Å: Chain C: L.40, N.42, Y.45, N.47, S.48, S.49 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.42 Hydrogen bonds: C:N.47 NAG.23: 4 residues within 4Å: Chain C: E.35, N.36, N.37, N.54 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.36, C:N.37 NAG.24: 5 residues within 4Å: Chain C: I.156, Q.189, N.191, T.193, E.194 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.156 Hydrogen bonds: C:N.191, C:T.193, C:E.194, C:E.194 Water bridges: C:T.227, C:T.227 NAG.25: 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.26: 4 residues within 4Å: Chain C: A.281, N.283, S.311, R.558 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.558, C:D.640 NAG.29: 4 residues within 4Å: Chain D: Y.45, N.47, S.48, S.49 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.47, D:S.49 NAG.30: 3 residues within 4Å: Chain B: V.250 Chain D: P.240, N.241 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:N.241, 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 SO4.20: 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 SO4.27: 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 SO4.31: 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

4 x AES: 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE(Covalent)

AES.15: 6 residues within 4Å: Chain A: E.167, E.168, F.319, Y.509, Y.624, Y.628 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.319, A:Y.628 Hydrogen bonds: A:E.168 AES.21: 7 residues within 4Å: Chain B: R.87, E.167, E.168, F.319, Y.509, Y.624, Y.628 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.319 Hydrogen bonds: B:Y.624, B:Y.624 AES.28: 7 residues within 4Å: Chain C: R.87, E.167, E.168, F.319, Y.509, Y.624, Y.628 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.319 Hydrogen bonds: C:E.167, C:E.168, C:Y.624 AES.32: 6 residues within 4Å: Chain D: E.167, E.168, F.319, Y.509, Y.624, Y.628 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.319, D:Y.628 Hydrogen bonds: D:E.167, D:Y.624, D:Y.624

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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