SMTL ID : 3deq.2 (2 other biounits)

Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: K.159, D.188, N.190, E.216, D.241, N.263 Ligands: LEU.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.188, A:E.216, A:D.241, LEU.3, H2O.1 MG.4: 7 residues within 4Å: Chain B: K.159, D.188, E.216, D.241, N.263, K.265 Ligands: LEU.6 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.188, B:E.216, B:D.241, LEU.6, H2O.6

2 x ALA: ALANINE(Non-covalent)

ALA.2: 10 residues within 4Å: Chain A: F.20, T.134, K.159, K.161, C.292, M.293, D.317, D.319, M.323 Ligands: LEU.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.20 Hydrogen bonds: A:T.134, A:K.161, A:D.319 ALA.5: 10 residues within 4Å: Chain B: F.20, T.134, K.159, K.161, C.292, M.293, D.317, D.319, M.323 Ligands: LEU.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.159, B:K.161, B:D.319

2 x LEU: LEUCINE(Non-covalent)

LEU.3: 14 residues within 4Å: Chain A: F.20, I.22, R.54, K.159, K.161, D.188, N.190, D.241, K.265, C.292, M.293, D.317 Ligands: MG.1, ALA.2 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.20, A:I.22 Hydrogen bonds: A:N.190, A:K.265, A:C.292 Water bridges: A:R.54, A:K.159, A:E.242, A:N.263 Salt bridges: A:K.159, A:K.161, A:K.265 LEU.6: 13 residues within 4Å: Chain B: F.20, I.22, K.159, K.161, D.188, N.190, D.241, K.265, C.292, M.293, D.317 Ligands: MG.4, ALA.5 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:F.20, B:I.22 Hydrogen bonds: B:N.190, B:K.265, B:C.292, B:D.317 Water bridges: B:R.54, B:E.216, B:N.263, B:C.292 Salt bridges: B:K.159, B:K.161, B:K.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalyanaraman, C. et al., Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure (2008)

Release Date

2008-11-25

Peptides

Muconate cycloisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Muconate cycloisomerase

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