SMTL ID : 1y79.1

Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp in Complex with a Peptidic Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.469, H.473, E.498, S.501, Y.614 Ligands: TRP.3 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain A Metal complexes: TRP.3, A:H.469, A:H.473, A:E.498, A:E.498

1 x LYS: LYSINE(Non-covalent)

LYS.2: 7 residues within 4Å: Chain A: W.425, M.426, E.470, H.473, G.606, Y.607 Ligands: TRP.3 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain A Hydrogen bonds: W.3, A:M.426, A:G.606, A:G.606, A:Y.607 Hydrophobic interactions: A:Y.607

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 14 residues within 4Å: Chain A: A.424, W.425, H.469, E.470, H.473, E.498, A.600, H.601, G.605, Y.607, Y.614 Ligands: ZN.1, LYS.2, GLY.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.607, A:Y.607 Hydrogen bonds: A:E.470, A:Y.607, A:Y.607 Water bridges: A:G.422, A:A.424 Salt bridges: A:H.469, A:H.473

1 x GLY: GLYCINE(Non-covalent)

GLY.4: 6 residues within 4Å: Chain A: H.469, E.470, H.601, Y.614 Ligands: TRP.3, ASP.5 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: D.5 Water bridges: A:N.222, A:R.593

1 x ASP: ASPARTIC ACID(Non-covalent)

ASP.5: 7 residues within 4Å: Chain A: L.550, R.593, Y.594, H.601, Y.611, Y.614 Ligands: GLY.4 10 PLIP interactions: 6 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.614 Hydrogen bonds: A:Y.611, G.4, D.5, D.5, D.5 Water bridges: A:Y.594 Salt bridges: A:R.593, A:R.593, A:H.601

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Comellas-Bigler, M. et al., Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp: Further Indication of a Ligand-dependant Hinge Movement Mechanism. J.Mol.Biol. (2005)

Release Date

2005-05-24

Peptides

Peptidyl-Dipeptidase Dcp: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

Peptidyl-Dipeptidase Dcp