SMTL ID : 5x7m.1

Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 14 residues within 4Å: Chain A: K.75, H.117, R.164, H.214, H.216, G.256, G.257, Y.258, E.299, P.300, G.301, R.302, Y.404 Chain B: C.374 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.75 Hydrogen bonds: A:G.257, A:Y.258, A:E.299, A:G.301, A:R.302, A:Y.404 Salt bridges: A:K.75, A:H.216, A:R.302 pi-Stacking: A:H.216 PLP.2: 14 residues within 4Å: Chain A: C.374 Chain B: A.73, K.75, D.94, H.117, R.164, H.216, G.256, G.257, Y.258, E.299, G.301, R.302, Y.404 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:K.75 Hydrogen bonds: B:D.94, B:R.164, B:G.257, B:Y.258, B:E.299, B:G.301, B:R.302 Salt bridges: B:K.75, B:H.216, B:R.302 pi-Stacking: B:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Son, H.F. et al., Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum. Biochem. Biophys. Res. Commun. (2018)

Release Date

2018-01-10

Peptides

Diaminopimelate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Diaminopimelate decarboxylase

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