SMTL ID : 4xew.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a HTS lead compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: W.85, S.143, G.144, S.145, Y.177, H.178, G.179, E.240, D.274, I.276, A.277, K.303 Chain B: P.337, T.338 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.240, A:I.276, A:K.303 Hydrogen bonds: A:G.144, A:S.145, A:K.303, B:G.336, B:T.338, B:T.338 Water bridges: A:D.142, A:S.143, A:S.143, A:S.145, A:D.180, A:E.240, A:K.303 pi-Stacking: A:Y.177 PLP.3: 14 residues within 4Å: Chain A: P.337, T.338 Chain B: W.85, S.143, G.144, S.145, Y.177, H.178, G.179, E.240, D.274, I.276, A.277, K.303 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.177, B:E.240, B:I.276 Hydrogen bonds: B:G.144, B:S.145, B:S.145, B:K.303, A:T.338, A:T.338, A:T.338 Water bridges: B:S.143, B:Y.177, B:D.180, B:E.240, A:F.339 pi-Stacking: B:Y.177

2 x 40N: 6-(2-fluorophenyl)[1,3]dioxolo[4,5-g]quinolin-8(5H)-one(Non-covalent)

40N.2: 13 residues within 4Å: Chain A: P.44, Y.45, W.84, Y.177, A.246, R.420, F.422 Chain B: M.111, F.112, G.113, G.336, P.337, T.338 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:F.112, B:G.113, A:R.420 Water bridges: B:G.336 Hydrophobic interactions: A:P.44, A:Y.177, A:F.422, A:F.422 pi-Stacking: A:Y.45, A:W.84, A:W.84, A:W.84 40N.4: 13 residues within 4Å: Chain A: M.111, F.112, G.113, G.336, P.337, T.338 Chain B: P.44, Y.45, W.84, Y.177, G.192, A.246, F.422 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:F.112, A:G.113, A:G.336 Hydrophobic interactions: B:P.44, B:Y.177, B:F.422 pi-Stacking: B:Y.45, B:W.84, B:W.84, B:W.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, R. et al., Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium tuberculosis BioA. J.Med.Chem. (2015)

Release Date

2015-07-08

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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