SMTL ID : 3ijl.1 (1 other biounit)

Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Pro-D-Glu; nonproductive substrate binding.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x PRO: PROLINE(Non-covalent)

PRO.1: 10 residues within 4Å: Chain A: F.16, K.153, C.281, M.282, T.283, D.303, D.305, G.306, L.309 Ligands: DGL.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.16, A:L.309 Hydrogen bonds: A:K.153, P.1, P.1 Water bridges: A:T.129 PRO.4: 10 residues within 4Å: Chain B: F.16, K.153, C.281, M.282, T.283, D.303, D.305, G.306, L.309 Ligands: DGL.5 7 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain B Hydrogen bonds: P.4, P.4, B:K.153 Hydrophobic interactions: B:F.16, B:T.283, B:L.309 Water bridges: B:T.129

2 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.2: 10 residues within 4Å: Chain A: F.16, V.18, R.23, P.47, Y.49, K.253, C.281, M.282, T.283 Ligands: PRO.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.16, A:V.18 Hydrogen bonds: A:C.281, A:C.281, A:T.283 Water bridges: A:Y.49, A:D.179, A:N.181, A:N.251, A:N.251, A:K.253, A:K.253, A:C.281, A:C.281 Salt bridges: A:R.23, A:K.153, A:K.253 DGL.5: 11 residues within 4Å: Chain B: F.16, V.18, R.23, P.47, Y.49, K.253, C.281, M.282, T.283, D.303 Ligands: PRO.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.16, B:V.18 Hydrogen bonds: B:C.281, B:C.281, B:T.283, B:D.303 Water bridges: B:Y.49, B:D.179, B:D.179, B:D.179, B:N.251, B:N.251, B:K.253, B:K.253, B:C.281, B:C.281 Salt bridges: B:R.23, B:K.153, B:K.253

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.179, E.206, D.231 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.179, A:E.206, A:D.231, H2O.3, H2O.4, H2O.6 MG.6: 5 residues within 4Å: Chain B: D.179, N.181, E.206, D.231, K.253 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.179, B:E.206, B:D.231, H2O.12, H2O.15, H2O.15

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

2010-07-21

Peptides

Muconate cycloisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Muconate cycloisomerase

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