SMTL ID : 4wye.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 1.75 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 13 residues within 4Å: Chain A: 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: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:E.240, A:I.276, A:K.303 Hydrogen bonds: A:G.144, A:S.145, A:S.145, A:K.303, B:T.338, B:T.338 Water bridges: A:S.143, A:S.145, A:S.145, A:Y.177, A:Y.177, A:E.240 Salt bridges: A:K.303 pi-Stacking: A:Y.177 PLP.6: 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 17 PLIP interactions: 3 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:T.338, A:T.338, B:S.143, B:G.144, B:S.145, B:K.303 Water bridges: A:F.339, B:S.143, B:S.145, B:S.145, B:Y.177, B:E.240 Hydrophobic interactions: B:E.240, B:I.276, B:K.303 Salt bridges: B:K.303 pi-Stacking: B:Y.177

2 x 3VW: phenyl(piperidin-4-yl)methanone(Non-covalent)

3VW.2: 12 residues within 4Å: Chain A: Y.45, W.84, W.85, Y.177, G.245, A.246, M.249, K.303, F.422, Y.427 Chain B: G.336, T.338 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.84, A:W.85, A:A.246 Hydrogen bonds: A:Y.45, A:Y.177, A:K.303, B:G.336 pi-Stacking: A:F.422 3VW.5: 11 residues within 4Å: Chain A: G.336 Chain B: Y.45, W.84, W.85, Y.177, G.245, A.246, M.249, K.303, F.422, Y.427 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.84, B:A.246, B:F.422, B:Y.427, B:Y.427 Hydrogen bonds: B:Y.45, B:Y.177, B:K.303, A:G.336

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 10 residues within 4Å: Chain A: P.44, Y.45, S.46, S.47, E.51, W.84, L.405, R.420 Chain B: G.113, G.114 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.44, A:S.47, A:E.51, A:E.51 Water bridges: A:R.420, B:G.114 Salt bridges: A:R.420 EPE.7: 8 residues within 4Å: Chain A: G.113, G.114 Chain B: P.44, Y.45, E.51, W.84, L.405, R.420 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Water bridges: A:G.114 Hydrogen bonds: B:P.44, B:P.44 Salt bridges: B:E.51, B:E.51, B:R.420

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: R.255, H.291, A.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.291

1 x ACN: ACETONE(Non-covalent)

ACN.8: 6 residues within 4Å: Chain B: Y.158, W.159, E.268, V.269, L.270, D.320 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.159, B:L.270

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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