SMTL ID : 6hp8.1 (1 other biounit)

Crystal structure of DPP8 in complex with Val-BoroPro

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x GK2: [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid(Covalent)

GK2.1: 12 residues within 4Å: Chain A: R.160, E.275, E.276, Y.669, Q.673, S.755, Y.756, V.781, Y.787, Y.791, N.835, H.865 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.781, A:Y.791 Hydrogen bonds: A:R.160, A:E.275, A:Y.669, A:Y.669, A:Y.669, A:Y.756, A:Y.787, A:Y.787, A:N.835 GK2.8: 12 residues within 4Å: Chain B: R.160, E.275, E.276, Y.669, Q.673, S.755, Y.756, V.781, Y.787, Y.791, N.835, H.865 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.781, B:Y.791 Hydrogen bonds: B:R.160, B:Y.669, B:Y.669, B:Y.756, B:Y.787, B:Y.787, B:N.835

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: R.158, Q.274, E.275, D.278, Y.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.274, A:Y.280 Water bridges: A:D.278 NA.9: 5 residues within 4Å: Chain B: R.158, Q.274, E.275, D.278, Y.280 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.275 Water bridges: B:D.278, B:Y.280

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: H.315, H.837, F.838 Chain B: T.317, R.324, A.326, F.831 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.837 Water bridges: A:T.317, A:T.317 GOL.4: 6 residues within 4Å: Chain A: H.188, L.206, V.207, E.208, I.241, R.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.188, A:E.208 Water bridges: A:R.244 GOL.5: 8 residues within 4Å: Chain A: G.526, S.527, N.528, I.529, Q.530, E.541, C.575, I.577 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.528, A:Q.530, A:C.575, A:I.577 GOL.6: 6 residues within 4Å: Chain A: N.448, R.524, H.525, Q.673, R.794, Y.795 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.525, A:R.794 Water bridges: A:I.449, A:I.449, A:R.524 GOL.7: 7 residues within 4Å: Chain A: W.383, T.384, P.385, W.391, F.453, H.454, V.455 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.384, A:F.453, A:V.455 GOL.10: 8 residues within 4Å: Chain A: T.317, R.324, A.326, F.831 Chain B: H.315, H.837, F.838 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.837 Water bridges: B:T.317, B:T.317 GOL.11: 6 residues within 4Å: Chain B: H.188, L.206, V.207, E.208, I.241, R.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.188, B:E.208 Water bridges: B:R.244 GOL.12: 8 residues within 4Å: Chain B: G.526, S.527, N.528, I.529, Q.530, E.541, C.575, I.577 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.528, B:Q.530, B:C.575, B:I.577 GOL.13: 6 residues within 4Å: Chain B: N.448, R.524, H.525, Q.673, R.794, Y.795 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.525, B:R.794 Water bridges: B:I.449, B:I.449, B:R.524, B:Y.795 GOL.14: 7 residues within 4Å: Chain B: W.383, T.384, P.385, W.391, F.453, H.454, V.455 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.384, B:F.453, B:V.455

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ross, B.H., Improvement of Protein Crystal Diffraction Using Post-Crystallization Methods: Infrared Laser Radiation Controls Crystal Order. Thesis (2019)

Release Date

2019-07-31

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dipeptidyl peptidase 8

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