SMTL ID : 6eop.2 (1 other biounit)

DPP8 - SLRFLYEG, space group 20

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x SER- LEU- ARG- PHE- LEU- TYR- GLU- GLY: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY(Non-covalent)

SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.1: 28 residues within 4Å: Chain A: M.76, R.160, G.162, E.275, E.276, H.525, Y.669, Q.673, V.674, K.685, W.754, S.755, Y.756, A.779, V.781, W.784, Y.787, Y.791, N.835, V.836, H.865, S.866, I.867, R.868, G.873, Y.876, E.877 Ligands: F15.5 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:W.754, A:Y.756, A:A.779, A:W.784, A:Y.787, A:Y.787, A:Y.791, A:V.836, A:I.867, A:I.867, A:I.867, A:Y.876 Hydrogen bonds: A:R.160, A:E.275, A:Y.669, A:Q.673, A:S.755, A:Y.756, A:Y.787, A:N.835, A:H.865, A:H.865, A:I.867 Water bridges: A:E.276 pi-Stacking: A:W.754, A:H.865 SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.2: 25 residues within 4Å: Chain B: M.76, R.160, E.275, E.276, Y.669, Q.673, V.674, K.685, W.754, S.755, Y.756, V.781, W.784, Y.787, Y.791, N.835, V.836, H.865, S.866, I.867, R.868, G.873, Y.876, E.877 Ligands: F15.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:W.754, B:Y.756, B:W.784, B:Y.787, B:Y.787, B:Y.791, B:V.836, B:I.867, B:I.867, B:I.867, B:Y.876 Hydrogen bonds: B:R.160, B:E.276, B:Q.673, B:S.755, B:Y.756, B:Y.787, B:N.835, B:H.865, B:H.865, B:I.867, B:E.877 Water bridges: B:R.160 Salt bridges: B:K.685 pi-Stacking: B:W.754, B:H.865

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: R.158, Q.274, E.275, D.278, Y.280 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:R.158, A:Q.274, A:D.278, A:Y.280 CA.4: 5 residues within 4Å: Chain B: R.158, Q.274, E.275, D.278, Y.280 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:R.158, B:Q.274, B:D.278, B:Y.280, H2O.10

2 x F15: PENTADECANOIC ACID(Non-covalent)

F15.5: 12 residues within 4Å: Chain A: F.667, Y.669, V.674, Y.686, R.688, W.754, Y.876, E.877, L.880, L.881 Ligands: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.1, SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.667, A:Y.669, A:Y.686, A:R.688, A:L.880, A:L.881 Hydrogen bonds: A:Y.686, A:Y.686 Salt bridges: A:K.685 F15.6: 9 residues within 4Å: Chain B: F.667, L.676, K.685, Y.686, R.688, Y.876, L.880 Ligands: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.2, SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.2 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.667, B:R.688, B:L.880 Hydrogen bonds: B:Y.686 Salt bridges: B:K.685

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ross, B. et al., Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-02-07

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Dipeptidyl peptidase 8

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