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

Crystal structure of DPP8 in complex with 1G244

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.1: 7 residues within 4Å: Chain A: T.322, R.329, R.330, A.331 Chain B: H.320, T.322 Ligands: TMO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.330 TMO.5: 9 residues within 4Å: Chain A: H.320, V.321, T.322, H.842 Chain B: T.322, R.329, R.330, A.331 Ligands: TMO.1 No protein-ligand interaction detected (PLIP)

2 x 9XH: (2~{S})-2-azanyl-4-[4-[bis(4-fluorophenyl)methyl]piperazin-1-yl]-1-(1,3-dihydroisoindol-2-yl)butane-1,4-dione(Non-covalent)

9XH.2: 18 residues within 4Å: Chain A: R.165, E.280, E.281, H.530, Y.674, Q.678, V.679, L.681, Y.691, S.760, Y.761, V.786, W.789, Y.792, Y.796, N.840, V.841, H.870 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.165, A:R.165, A:V.679, A:Y.761, A:V.786, A:V.786, A:W.789, A:Y.796, A:V.841 Hydrogen bonds: A:R.165, A:E.280, A:E.281, A:Q.678, A:Y.792, A:N.840 9XH.6: 17 residues within 4Å: Chain B: R.165, E.280, E.281, H.530, Y.674, V.679, L.681, Y.691, S.760, Y.761, V.786, W.789, Y.792, Y.796, N.840, V.841, H.870 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.165, B:V.679, B:Y.761, B:V.786, B:W.789, B:Y.796, B:V.841 Hydrogen bonds: B:R.165, B:E.281, B:Y.674, B:Y.792, B:N.840

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

NA.3: 5 residues within 4Å: Chain A: R.163, Q.279, E.280, D.283, Y.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.285, A:Y.285 NA.7: 6 residues within 4Å: Chain B: R.163, R.165, Q.279, E.280, D.283, Y.285 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.280

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 10 residues within 4Å: Chain A: S.532, N.533, I.534, Y.544, F.545, E.546, L.557, C.580, C.581, I.582 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.533, A:C.580, A:I.582 PO4.8: 10 residues within 4Å: Chain B: S.532, N.533, I.534, Q.535, F.545, E.546, L.557, C.580, C.581, I.582 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.533, B:N.533, B:N.533, B:C.580, B:I.582

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ross, B. et al., Aerosol-based ligand soaking of reservoir-free protein crystals. J.Appl.Crystallogr. (2021)

Release Date

2021-01-13

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Dipeptidyl peptidase 8

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