SMTL ID : 4wyf.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a DSF fragment hit

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

1 x 3VX: N-(1-oxo-1H-inden-5-yl)acetamide(Non-covalent)

3VX.1: 9 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 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.44, B:Y.45, B:W.84 pi-Stacking: B:W.84, B:W.84 Hydrogen bonds: A:F.112, A:G.113

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

PLP.2: 14 residues within 4Å: Chain A: W.84, 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 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.84, A:Y.177, A:E.240, A:I.276 Hydrogen bonds: A:G.144, A:S.145, A:K.303, B:T.338, B:T.338 Water bridges: A:S.145, A:S.145, A:Y.177, A:D.180, A:E.240, B:F.339 pi-Stacking: A:Y.177 PLP.3: 13 residues within 4Å: Chain A: P.337, T.338 Chain B: 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, B:K.303 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:D.180, B:E.240, A:F.339 Salt bridges: B:K.303 pi-Stacking: B:Y.177

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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