SMTL ID : 1hkv.1

mycobacterium diaminopimelate dicarboxylase (lysa)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 5 residues within 4Å: Chain A: K.72, S.216, R.303, R.344 Chain B: E.376 4 PLIP interactions: 4 interactions with chain A, Hydrogen bonds: A:K.72, A:S.216 Salt bridges: A:R.303, A:R.344 LYS.3: 12 residues within 4Å: Chain A: C.375, E.376, S.377, Y.413 Chain B: K.72, H.213, S.216, R.303, R.344, Y.348, Y.405 Ligands: PLP.4 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, Hydrogen bonds: B:S.216, B:S.216, A:S.377, A:S.377, A:Y.413 Salt bridges: B:R.303, B:R.344

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

PLP.2: 15 residues within 4Å: Chain A: A.70, K.72, H.114, R.161, H.211, H.213, S.216, G.257, G.258, E.300, P.301, G.302, R.303, Y.405 Chain B: C.375 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.70, A:K.72 Hydrogen bonds: A:K.72, A:G.257, A:G.258, A:E.300, A:G.302, A:R.303, A:Y.405, A:Y.405 Water bridges: A:R.303, A:R.303 Salt bridges: A:K.72, A:R.303 pi-Stacking: A:H.213 PLP.4: 15 residues within 4Å: Chain A: C.375 Chain B: A.70, K.72, H.114, R.161, H.213, S.216, G.257, G.258, E.300, P.301, G.302, R.303, Y.405 Ligands: LYS.3 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:K.72, K.3 Hydrogen bonds: B:K.72, B:S.216, B:G.258, B:E.300, B:G.302, B:R.303 Water bridges: B:R.303 Salt bridges: B:K.72, B:R.303 pi-Stacking: B:H.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gokulan, K. et al., Crystal Structure of Mycobacterium Tuberculosis Diaminopimelate Decarboxylase, an Essential Enzyme in Bacterial Lysine Biosynthesis. J.Biol.Chem. (2003)

Release Date

2003-03-20

Peptides

DIAMINOPIMELATE DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DIAMINOPIMELATE DECARBOXYLASE

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