SMTL ID : 5e3a.1

Structure of human DPP3 in complex with opioid peptide leu-enkephalin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x TYR- GLY- GLY- PHE- LEU: Leu-enkephalin(Non-covalent)

TYR-GLY-GLY-PHE-LEU.1: 19 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, H.455, W.495, E.507, E.508, H.568, R.572 Ligands: ZN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.109, A:N.391, A:H.455 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.572, A:R.572

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-LEU.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.450, A:H.455, A:E.508, A:E.508

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.12 MG.4: 5 residues within 4Å: Chain A: G.162, L.163, G.164, G.167, T.169 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.162, A:G.164, A:G.167, H2O.5, H2O.6

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 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.317, A:G.323, A:D.496, H2O.1, H2O.2

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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