SMTL ID : 6eop.1 (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: 27 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, 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: F15.4 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:W.754, A:Y.756, 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:H.525, A:Y.669, A:Q.673, A:S.755, A:Y.756, A:Y.787, A:Y.787, A:N.835, A:H.865, A:H.865, A:I.867 Water bridges: A:E.275, A:E.276 pi-Stacking: A:W.754, A:H.865 SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.5: 27 residues within 4Å: Chain B: 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, 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: F15.8 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.275, B:H.525, 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:E.275 pi-Stacking: B:W.754, B:H.865

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 6 residues within 4Å: Chain A: H.172, P.222, A.223, P.287, K.288, A.289 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:P.222, A:P.287, A:K.288, A:A.289 Salt bridges: A:H.172, A:H.172, A:K.288, A:K.288 FLC.6: 6 residues within 4Å: Chain B: H.172, P.222, A.223, P.287, K.288, A.289 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:P.222, B:P.287, B:K.288, B:A.289 Salt bridges: B:H.172, B:H.172, B:K.288, B:K.288

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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.158, A:Q.274, A:D.278, A:Y.280, H2O.1 CA.7: 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)

F15.4: 12 residues within 4Å: Chain A: F.667, Y.669, V.674, L.676, K.685, Y.686, R.688, W.754, Y.876, E.877, L.880 Ligands: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.667, A:Y.669, A:L.676, A:R.688, A:L.880 Salt bridges: A:K.685 F15.8: 12 residues within 4Å: Chain B: F.667, Y.669, V.674, L.676, K.685, Y.686, R.688, W.754, Y.876, E.877, L.880 Ligands: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.667, B:Y.669, B:L.676, B:R.688, B:L.880 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
A

B
A

Dipeptidyl peptidase 8

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