SMTL ID : 3k1g.10 (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

homo-dimer

Ligands

2 x SER: SERINE(Non-covalent)

SER.1: 11 residues within 4Å: Chain A: F.19, T.134, K.159, K.161, C.292, M.293, A.294, D.318, D.320 Ligands: TYR.2, GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.134, A:K.159, A:K.161, A:D.320 SER.5: 11 residues within 4Å: Chain B: F.19, T.134, K.159, K.161, C.292, M.293, A.294, D.318, D.320 Ligands: TYR.6, GOL.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.134, B:K.161, B:D.318 Water bridges: B:C.292

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: SER.1, MG.4 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.19, A:I.21, A:I.54, A:A.294 Hydrogen bonds: A:N.191, A:N.191, A:C.292 Water bridges: A:N.262, A:C.292 Salt bridges: A:K.159, A:K.161, A:K.264 TYR.6: 17 residues within 4Å: Chain B: 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: SER.5, MG.8 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:I.21, B:F.53, B:I.54 Hydrogen bonds: B:N.191, B:K.264, B:C.292 Water bridges: B:N.262, B:C.292 Salt bridges: B:K.159, B:K.161, B:K.264

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: L.15, T.134, D.320, A.321, G.324 Ligands: SER.1 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: S.1, S.1, A:T.134, A:T.134 GOL.7: 6 residues within 4Å: Chain B: L.15, T.134, A.294, D.320, G.324 Ligands: SER.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:T.134, B:A.294, S.5, S.5

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: K.159, 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 MG.8: 4 residues within 4Å: Chain B: D.189, E.215, D.240 Ligands: TYR.6 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B Metal complexes: TYR.6, TYR.6, B:D.189, B:E.215, B:D.240

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Dipeptide Epimerase

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