SMTL ID : 5e33.1

Structure of human DPP3 in complex with met-enkephalin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x TYR- GLY- GLY- PHE- MET: Met-enkephalin(Non-covalent)

TYR-GLY-GLY-PHE-MET.1: 21 residues within 4Å: Chain A: F.109, E.316, Y.318, I.386, P.387, A.388, G.389, I.390, N.391, I.392, N.394, R.399, A.416, F.443, H.455, E.507, E.508, H.568, R.572, R.669 Ligands: ZN.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.109, A:P.387, A:H.455, A:E.507 Hydrogen bonds: A:E.316, A:Y.318, A:A.388, A:G.389, A:G.389, A:N.391, A:N.394, A:H.568, A:R.669 Water bridges: A:R.399, A:W.495 Salt bridges: A:R.669 pi-Cation interactions: A:H.455

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.450, H.455, E.508 Ligands: TYR-GLY-GLY-PHE-MET.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.17

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.101, N.102, S.108, S.384, G.385 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.108, A:S.384, H2O.15 MG.4: 5 residues within 4Å: Chain A: G.162, L.163, G.164, G.167, T.169 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.164, A:G.167, H2O.5, H2O.10, H2O.14

1 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: S.317, G.323, D.496, A.503, S.504 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.317, A:G.323, A:D.496, A:S.504

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition. Sci Rep (2016)

Release Date

2016-04-13

Peptides

Dipeptidyl peptidase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dipeptidyl peptidase 3

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