SMTL ID : 3kum.4 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ARG: ARGININE(Non-covalent)

ARG.1: 8 residues within 4Å: Chain A: F.19, T.134, K.159, K.161, C.292, D.318, D.320 Ligands: TYR.2 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:F.19 Hydrogen bonds: A:T.134, A:K.159, A:K.161, A:D.320 Water bridges: A:A.294 Salt bridges: A:D.320 pi-Cation interactions: A:F.19 ARG.4: 7 residues within 4Å: Chain B: F.19, T.134, K.161, C.292, D.318, D.320 Ligands: TYR.5 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:F.19 Hydrogen bonds: B:T.134, B:K.161, B:D.320 Water bridges: B:C.292, R.4, R.4 Salt bridges: B:D.320 pi-Cation interactions: B:F.19

2 x TYR: TYROSINE(Non-covalent)

TYR.2: 18 residues within 4Å: Chain A: F.19, 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: ARG.1, MG.3 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.19, A:F.19, A:I.21, A:F.53, A:I.54 Hydrogen bonds: A:N.191, A:N.191, A:D.240, A:C.292, A:A.294 Water bridges: A:N.262, A:K.264, A:C.292 Salt bridges: A:K.159, A:K.161, A:K.264 TYR.5: 16 residues within 4Å: Chain B: F.19, I.21, I.26, F.53, K.159, K.161, D.189, N.191, E.215, D.240, K.264, C.292, A.294, E.295 Ligands: ARG.4, MG.6 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:F.19, B:I.21, B:F.53, B:F.53, B:A.294 Hydrogen bonds: B:N.191, B:N.191, B:C.292 Water bridges: B:K.264, B:K.264, B:C.292 Salt bridges: B:K.159, B:K.161, B:K.264

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: K.159, K.161, 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 MG.6: 6 residues within 4Å: Chain B: K.159, D.189, N.191, E.215, D.240 Ligands: TYR.5 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.189, B:E.215, B:D.240, TYR.5, H2O.5

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

2010-10-13

Peptides

Dipeptide Epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Dipeptide Epimerase

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