SMTL ID : 3c5q.1

Crystal structure of diaminopimelate decarboxylase (I148L mutant) from Helicobacter pylori complexed with L-lysine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 14 residues within 4Å: Chain A: A.64, K.66, D.85, H.205, S.208, G.244, G.245, E.279, P.280, G.281, R.282, Y.378 Chain B: C.349 Ligands: LYS.2 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:K.66, A:H.205, K.2 Hydrogen bonds: A:G.245, A:E.279, A:G.281, A:R.282 Water bridges: A:R.155, A:R.282 Salt bridges: A:H.205 pi-Stacking: A:H.205 PLP.4: 14 residues within 4Å: Chain A: C.349 Chain B: A.64, K.66, D.85, H.205, S.208, G.244, G.245, E.279, P.280, G.281, R.282, Y.378 Ligands: LYS.5 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:K.66, B:H.205, K.5 Hydrogen bonds: B:G.245, B:G.281, B:R.282, B:Y.378 Water bridges: B:R.155, B:R.282 Salt bridges: B:H.205 pi-Stacking: B:H.205

2 x LYS: LYSINE(Non-covalent)

LYS.2: 12 residues within 4Å: Chain A: K.66, L.168, S.208, R.282, R.318, Y.322, Y.378, M.382 Chain B: C.349, E.350, Y.386 Ligands: PLP.1 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:E.350, A:L.168, A:Y.378 Hydrogen bonds: B:E.350 Salt bridges: A:R.282, A:R.318 LYS.5: 12 residues within 4Å: Chain A: C.349, E.350, Y.386 Chain B: K.66, L.168, S.208, R.282, R.318, Y.322, Y.378, M.382 Ligands: PLP.4 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.168, B:Y.378, A:E.350 Hydrogen bonds: B:Y.322, A:E.350 Salt bridges: B:R.282, B:R.318

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: L.121, N.124, I.125, F.127, L.128, K.149, A.150, R.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.124, A:L.128, A:K.149, A:R.151 GOL.6: 8 residues within 4Å: Chain B: L.121, N.124, I.125, F.127, L.128, K.149, A.150, R.151 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.124, B:L.128, B:K.149, B:R.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, T. et al., Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori. To be Published

Release Date

2008-05-27

Peptides

Diaminopimelate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diaminopimelate decarboxylase