SMTL ID : 3lv2.1

Crystal structure of Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase in complex with substrate analog sinefungin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: W.90, S.148, G.149, S.150, Y.182, H.183, G.184, E.245, D.279, I.281, A.282, K.308 Chain B: P.342, T.343 Ligands: SFG.2 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:T.343, B:T.343, B:T.343, A:G.149, A:S.150, A:S.150 Water bridges: B:F.344, A:S.148, A:E.245 Hydrophobic interactions: A:E.245, A:I.281, A:K.308 Salt bridges: A:K.308 pi-Stacking: A:Y.182 PLP.3: 14 residues within 4Å: Chain A: P.342, T.343 Chain B: W.90, S.148, G.149, S.150, Y.182, H.183, G.184, E.245, D.279, I.281, A.282, K.308 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.245, B:I.281, B:K.308 Hydrogen bonds: B:G.149, B:S.150, A:T.343, A:T.343, A:T.343 Water bridges: B:S.150, B:Y.182, B:Y.182, B:Y.182, B:Y.182, B:D.185, B:E.245, A:F.344 Salt bridges: B:K.308 pi-Stacking: B:Y.182

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.2: 15 residues within 4Å: Chain A: Y.50, W.89, W.90, Y.182, A.251, K.308, V.408, L.410, R.425, P.426, F.427, R.428 Chain B: R.340, G.341 Ligands: PLP.1 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.90, A:A.251 Hydrogen bonds: A:Y.182, A:L.410, A:R.425, A:R.428, B:G.341 Water bridges: A:W.89, A:R.425, B:T.343 Salt bridges: A:K.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dey, S. et al., Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Biochemistry (2010)

Release Date

2010-08-25

Peptides

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase