SMTL ID : 7xnm.1

Structure of porcine dipeptidyl peptidase 4 inhibitory peptide complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.58 Å

Oligo State

homo-dimer

Ligands

2 x ILE- LEU- ALA- PRO- PRO- GLU- ARG: ILE-LEU-ALA-PRO-PRO-GLU-ARG(Non-covalent)

ILE-LEU-ALA-PRO-PRO-GLU-ARG.1: 13 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, G.703 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:E.167, B:Y.593, B:Y.628 Hydrogen bonds: B:R.87, B:Y.509, B:Y.509, B:S.592, B:Y.624 ILE-LEU-ALA-PRO-PRO-GLU-ARG.2: 16 residues within 4Å: Chain A: Y.10, R.87, E.167, E.168, Y.509, R.522, L.523, S.524, W.525, W.589, S.592, Y.624, N.672, H.702, G.703, Y.714 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.509 Hydrogen bonds: A:R.87, A:Y.509, A:Y.509, A:S.592, A:S.592 Salt bridges: A:E.507

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.3: 9 residues within 4Å: Chain A: R.559, G.561, T.562, F.563, E.566, M.600, Y.644, N.647, R.653 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.559, A:R.559, A:E.566

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

NAG-NAG.4: 5 residues within 4Å: Chain A: A.281, N.283, R.558, E.639, D.640 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.558, A:D.640, A:D.640 NAG-NAG.5: 3 residues within 4Å: Chain A: N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain B: R.559, G.561, T.562, E.566, Y.644, N.647, R.653 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.559, B:R.559, B:Y.644 NAG-NAG.8: 6 residues within 4Å: Chain B: A.281, N.283, T.312, R.558, E.639, D.640 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.558, B:E.639 NAG-NAG.9: 1 residues within 4Å: Chain B: N.241 No protein-ligand interaction detected (PLIP)

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

NAG.10: 1 residues within 4Å: Chain A: N.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.11: 5 residues within 4Å: Chain A: E.35, N.36, N.37, N.54, S.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.36, A:N.54 NAG.12: 6 residues within 4Å: Chain B: I.156, Q.189, N.191, T.193, E.194, K.229 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.194 Hydrogen bonds: B:T.193, B:K.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W.Y. et al., Structure of porcine dipeptidyl peptidase 4 inhibitory peptide complex. To Be Published

Release Date

2023-05-17

Peptides

Dipeptidyl peptidase 4 soluble form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4 soluble form

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