SMTL ID : 3tfu.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, post-reaction complex with a 3,6-dihydropyrid-2-one heterocycle inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x PL8: [5-hydroxy-4-({[6-(3-hydroxypropyl)-2-oxo-1,2-dihydropyridin-3-yl]amino}methyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

PL8.1: 19 residues within 4Å: Chain A: P.44, W.84, W.85, S.143, G.144, S.145, Y.177, H.178, G.179, E.240, D.274, I.276, K.303 Chain B: M.111, F.112, G.113, G.336, P.337, T.338 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.84 Hydrogen bonds: A:G.144, A:S.145, A:K.303, B:F.112, B:G.113, B:T.338, B:T.338 Water bridges: A:S.143, A:S.143, A:Y.177, A:D.180, A:D.180, B:F.339 PL8.2: 19 residues within 4Å: Chain A: P.337, T.338 Chain B: W.84, W.85, S.143, G.144, S.145, Y.177, H.178, G.179, E.240, A.246, D.274, I.276, A.277, K.303, F.422, Y.427 Ligands: DMS.3 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.276 Hydrogen bonds: B:G.144, B:S.145, A:T.338, A:T.338 Water bridges: B:S.143, B:Y.177, B:T.181, B:E.240, A:F.339 pi-Stacking: B:Y.177

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 6 residues within 4Å: Chain A: G.113, G.114 Chain B: P.44, W.84, R.420 Ligands: PL8.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:G.114 Hydrogen bonds: B:R.420

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, C. et al., Mechanism-based Inactivation by Aromatization of the Transaminase BioA Involved in Biotin Biosynthesis in Mycobaterium tuberculosis. J.Am.Chem.Soc. (2011)

Release Date

2011-10-19

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

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