SMTL ID : 4w1x.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with 1-(4-(4-(3-chlorobenzoyl)piperazin-1-yl)phenyl)ethanone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)(Non-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 18 PLIP interactions: 4 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:T.338, B:T.338, A:G.144, A:S.145 Water bridges: B:G.336, B:F.339, A:D.142, A:S.143, A:S.145, A:S.145, A:D.180, A:D.180, A:E.240 Hydrophobic interactions: A:Y.177, A:E.240, A:I.276 Salt bridges: A:K.303 pi-Stacking: A:Y.177 PLP.8: 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: 14 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:S.145, B:Y.177, B:D.180, B:E.240, A:F.339 Salt bridges: B:K.303 pi-Stacking: B:Y.177

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

EDO.2: 3 residues within 4Å: Chain A: A.370, G.371, A.374 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.440 EDO.4: 2 residues within 4Å: Chain A: R.213, D.387 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.387, A:R.389 Water bridges: A:R.213, A:R.213, A:D.214 EDO.7: 3 residues within 4Å: Chain B: V.242, P.254, H.291 No protein-ligand interaction detected (PLIP)

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

PEG.3: 3 residues within 4Å: Chain A: R.213, H.252, D.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.253, A:D.253 Water bridges: A:R.255

2 x 3G9: 1-{4-[4-(3-chlorobenzoyl)piperazin-1-yl]phenyl}ethanone(Non-covalent)

3G9.5: 17 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, G.176, Y.177, D.189, G.192, G.193, A.246, G.247, F.422 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.44, B:Y.45 pi-Stacking: B:W.84, B:W.84, B:Y.177 Halogen bonds: B:G.176 Hydrogen bonds: A:F.112, A:G.113 3G9.6: 15 residues within 4Å: Chain A: P.44, Y.45, W.84, G.176, Y.177, G.192, G.193, A.246, G.247 Chain B: M.111, F.112, G.113, G.336, P.337, T.338 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.44, A:P.44, A:Y.45 Water bridges: A:R.423 pi-Stacking: A:W.84, A:W.84, A:Y.177 Halogen bonds: A:G.176 Hydrogen bonds: B:F.112, B:G.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, S.W. et al., Target-Based Identification of Whole-Cell Active Inhibitors of Biotin Biosynthesis in Mycobacterium tuberculosis. Chem.Biol. (2015)

Release Date

2015-02-04

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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