SMTL ID : 3jw7.7 (7 other biounits)

Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Ile-L-Tyr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ILE: ISOLEUCINE(Non-covalent)

ILE.1: 10 residues within 4Å: Chain A: F.19, T.134, K.159, K.161, C.292, A.294, D.318, D.320 Ligands: TYR.2, GOL.3 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.19, A:A.294, Y.2 Hydrogen bonds: A:K.159, A:K.161, A:D.318

1 x TYR: TYROSINE(Non-covalent)

TYR.2: 17 residues within 4Å: Chain A: I.21, I.26, F.53, I.54, K.159, K.161, D.189, N.191, E.215, D.240, K.264, C.292, M.293, A.294, E.295 Ligands: ILE.1, MG.4 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.21, A:I.54, A:A.294, I.1 Hydrogen bonds: A:N.191, A:N.191, A:N.262, A:C.292, A:A.294, A:D.318 Water bridges: A:K.264, A:K.264, A:K.264, A:C.292 Salt bridges: A:K.159, A:K.161, A:K.264 pi-Stacking: A:F.53

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: L.15, F.19, D.320, A.321, F.323, G.324 Ligands: ILE.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.320, A:D.320, A:G.324 Water bridges: A:E.17, A:G.324

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: K.159, D.189, N.191, E.215, D.240 Ligands: TYR.2 5 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: TYR.2, A:D.189, A:E.215, A:D.240, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukk, T. et al., Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2010-08-11

Peptides

Dipeptide Epimerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

Dipeptide Epimerase

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