SMTL ID : 5te2.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 7B9: [5-hydroxy-4-({[6-(3-hydroxypropyl)-4-oxo-1,4-dihydropyridin-3-yl]amino}methyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

7B9.1: 15 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: G.336, P.337, T.338 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.84, A:W.84, A:E.240, A:I.276 Hydrogen bonds: A:S.143, A:G.144, A:S.145, A:K.303, A:K.303, B:G.336, B:T.338, B:T.338 Water bridges: A:S.143, A:D.180, A:D.180, B:F.339 pi-Stacking: A:Y.177 7B9.4: 17 residues within 4Å: Chain A: G.336, P.337, T.338 Chain B: Y.45, W.84, 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: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.45, B:W.84, B:E.240, B:I.276 Hydrogen bonds: B:G.144, B:S.145, B:K.303, A:G.336, A:T.338, A:T.338 Water bridges: B:S.143, B:S.145, B:S.145, B:D.180 pi-Stacking: B:W.84, B:Y.177

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: R.213, V.242, F.251, H.252, D.253, P.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.213 Water bridges: A:D.214

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

EDO.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 8 residues within 4Å: Chain B: R.213, V.242, F.251, H.252, D.253, P.254, H.291, C.391 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eiden, C.G. et al., Rational Optimization of Mechanism-Based Inhibitors through Determination of the Microscopic Rate Constants of Inactivation. J. Am. Chem. Soc. (2017)

Release Date

2017-05-31

Peptides

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

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