SMTL ID : 3k1g.6 (11 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x SER: SERINE(Non-covalent)

SER.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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.161, A:D.320

1 x TYR: TYROSINE(Non-covalent)

TYR.2: 16 residues within 4Å: Chain A: F.19, I.26, F.53, I.54, K.159, K.161, D.189, N.191, E.215, D.240, K.264, C.292, A.294, E.295 Ligands: SER.1, MG.4 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:F.19, A:I.54, A:A.294 Hydrogen bonds: A:N.191, A:C.292, A:D.318 Water bridges: A:K.264 Salt bridges: A:K.159, A:K.161, A:K.264

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: L.15, T.134, A.294, D.320, A.321 Ligands: SER.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:T.134, A:A.294, S.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: K.161, D.189, E.215, D.240 Ligands: TYR.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.189, A:E.215, A:D.240, TYR.2, 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

2010-08-18

Peptides

Dipeptide Epimerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

Dipeptide Epimerase

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