SMTL ID : 7oup.1

Structure of human DPP3 in complex with a hydroxyethylene transition state peptidomimetic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x VAL- 1QI- PRO- TRP: ((2R,4S,5S)-5-((S)-2-amino-3-methylbutanamido)-2-benzyl-4-hydroxy-6-methylheptanoyl)-L-prolyl-L-tryptophan(Non-covalent)

VAL-1QI-PRO-TRP.1: 24 residues within 4Å: Chain A: F.109, E.316, Y.318, I.386, P.387, A.388, G.389, I.390, N.391, N.394, R.399, V.412, A.416, V.447, H.450, H.455, E.508, E.512, H.568, R.572, R.669, K.670, I.672 Ligands: ZN.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.109, A:Y.318, A:P.387, A:A.388, A:I.390, A:A.416, A:V.447, A:H.568, A:R.669, A:K.670, A:I.672 Hydrogen bonds: A:E.316, A:Y.318, A:A.388, A:G.389, A:N.391, A:N.394, A:R.399, A:H.450, A:E.508, A:R.669 Salt bridges: A:R.669 pi-Cation interactions: A:R.669, A:K.670

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.450, H.455, E.508 Ligands: VAL-1QI-PRO-TRP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.450, A:H.455, A:E.508, H2O.2

1 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: S.317, G.323, D.496, S.504 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.317, A:G.323, A:D.496, A:S.504, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: G.162, L.163, G.164, G.167, I.168, T.169 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.162, A:G.164, A:G.167, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ivkovic, J. et al., Efficient Entropy-Driven Inhibition of Dipeptidyl Peptidase III by Hydroxyethylene Transition-State Peptidomimetics. Chemistry (2021)

Release Date

2021-08-11

Peptides

Dipeptidyl peptidase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dipeptidyl peptidase 3