SMTL ID : 6hp8.2 (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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.781, A:Y.791, A:Y.791 Hydrogen bonds: A:R.160, A:E.275, A:Y.669, A:Y.669, A:Y.756, A:Y.787, A:Y.787, A:N.835 Water bridges: A:Y.669 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 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.781, B:Y.791, 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: 4 residues within 4Å: Chain A: R.158, Q.274, D.278, Y.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.278, 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.280 Water bridges: B:D.278

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: T.317, R.324, R.325, A.326, F.831 Chain B: H.315, T.317, H.837 Ligands: GOL.10 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:R.324, B:T.317, B:T.317 Hydrogen bonds: B:H.837 GOL.4: 7 residues within 4Å: Chain A: H.188, N.205, L.206, V.207, E.208, I.241, R.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.208, A:E.208, A:I.241 GOL.5: 5 residues within 4Å: Chain A: W.383, W.391, F.453, H.454, V.455 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.383, A:H.454, A:V.455 GOL.6: 7 residues within 4Å: Chain A: N.448, I.449, R.524, H.525, Q.673, R.794, Y.795 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.449, A:I.449, A:R.794 Water bridges: A:Q.673, A:R.794 GOL.7: 7 residues within 4Å: Chain A: G.526, S.527, N.528, Q.530, E.541, C.575, I.577 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.528, A:Q.530, A:E.541, A:I.577 Water bridges: A:C.575 GOL.10: 9 residues within 4Å: Chain A: H.315, A.326, H.837 Chain B: T.317, R.324, R.325, A.326, F.831 Ligands: GOL.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.837 Water bridges: B:R.324 GOL.11: 5 residues within 4Å: Chain B: W.383, W.391, F.453, H.454, V.455 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.383, B:V.455 GOL.12: 7 residues within 4Å: Chain B: N.448, I.449, R.524, H.525, Q.673, R.794, Y.795 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.448, B:R.794, B:Y.795 Water bridges: B:I.449, B:R.794 GOL.13: 8 residues within 4Å: Chain B: G.526, S.527, N.528, I.529, E.541, C.575, C.576, I.577 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.526, B:N.528, B:Q.530, B:E.541, B:E.541, B:I.577 GOL.14: 5 residues within 4Å: Chain B: H.595, R.680, F.681, K.682, K.685 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.680, B:F.681, B:K.682 Water bridges: B:K.685

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
B

B
C

Dipeptidyl peptidase 8

Related Entries With Identical Sequence