SMTL ID : 4wyc.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a thiazole benzamide inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(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 18 PLIP interactions: 4 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:T.338, B:T.338, B:T.338, A:G.144, A:S.145, A:S.145 Water bridges: B:F.339, A:S.143, A:S.145, A:Y.177, A:Y.177, A:Y.177, A:E.240 Hydrophobic interactions: A:E.240, A:I.276, A:K.303 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 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:T.338, A:T.338, A:T.338, B:S.143, B:G.144, B:S.145 Water bridges: A:F.339, B:S.143, B:S.145, B:Y.177, B:Y.177, 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 3VS: 4-(1H-imidazol-1-yl)benzamide(Non-covalent)

3VS.2: 11 residues within 4Å: Chain A: P.44, Y.45, W.84, Y.177 Chain B: M.111, F.112, G.113, G.336, P.337, T.338 Ligands: SO4.5 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.44, A:Y.45 Hydrogen bonds: A:Y.177, B:F.112, B:G.113 pi-Stacking: A:W.84, A:W.84 3VS.7: 10 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 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.44 pi-Stacking: B:Y.45, B:W.84, B:W.84 Hydrogen bonds: A:G.113, A:P.337 Water bridges: A:F.112

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: T.131, P.132, A.133, D.290, S.295 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.133, A:S.295 Water bridges: A:I.130, A:T.131, A:D.290 EDO.9: 2 residues within 4Å: Chain B: R.70, I.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.70, B:R.70 Water bridges: B:D.414

1 x FOR: FORMYL GROUP(Non-covalent)

FOR.4: 4 residues within 4Å: Chain A: L.310, S.311 Chain B: L.310, S.311 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.311, B:S.311

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

SO4.5: 5 residues within 4Å: Chain A: P.44, R.420 Chain B: G.113, G.114 Ligands: 3VS.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.420, B:G.114 Salt bridges: A:R.420

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 2 residues within 4Å: Chain B: W.65, E.76 No protein-ligand interaction detected (PLIP)

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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