SMTL ID : 4w1v.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: S.117, G.118, S.119, Y.151, H.152, G.153, E.214, D.248, I.250, A.251, K.277 Chain B: P.311, T.312 Ligands: 3GS.2 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.214, A:I.250, A:K.277 Hydrogen bonds: A:G.118, A:S.119, A:K.277, B:T.312, B:T.312 Water bridges: A:S.117, A:S.119, A:Y.151, A:E.214, B:G.310, B:F.313 pi-Stacking: A:Y.151 PLP.4: 14 residues within 4Å: Chain A: P.311, T.312 Chain B: S.117, G.118, S.119, Y.151, H.152, G.153, E.214, D.248, I.250, A.251, K.277 Ligands: 3GS.5 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.214, B:I.250, B:K.277 Hydrogen bonds: B:G.118, B:S.119, B:S.119, B:K.277, A:T.312, A:T.312, A:T.312 Water bridges: B:S.117, B:E.214 Salt bridges: B:K.277 pi-Stacking: B:Y.151

2 x 3GS: dimethyl (2R)-5-(3-fluorophenyl)-1H-pyrrolo[1,2-c][1,3]thiazole-6,7-dicarboxylate 2-oxide(Non-covalent)

3GS.2: 13 residues within 4Å: Chain A: P.18, Y.19, W.58, Y.151, R.394, F.396 Chain B: M.85, F.86, G.87, G.310, P.311, T.312 Ligands: PLP.1 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:T.312 Hydrophobic interactions: A:P.18, A:P.18, A:Y.19, A:Y.19, A:W.58, A:W.58 Salt bridges: A:R.394 3GS.5: 14 residues within 4Å: Chain A: M.85, F.86, G.87, G.310, P.311, T.312 Chain B: P.18, Y.19, W.58, Y.151, A.220, K.277, R.394 Ligands: PLP.4 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.18, B:P.18, B:Y.19, B:Y.19, B:W.58, B:W.58 Hydrogen bonds: A:T.312

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

PEG.3: 6 residues within 4Å: Chain A: V.216, F.225, H.226, P.228, H.265, C.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.265 Water bridges: A:R.187

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

EDO.6: 9 residues within 4Å: Chain B: T.146, W.147, G.150, H.152, I.161, V.212, V.213, E.214, Q.218 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.146, B:T.146, B:E.214, B:E.214, B:Q.218 Water bridges: B:G.150 EDO.8: 4 residues within 4Å: Chain B: V.216, H.226, P.228, H.265 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.226 EDO.9: 4 residues within 4Å: Chain B: L.331, G.332, Q.333, D.334 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain B: R.240, Y.241 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.240

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 1 residues within 4Å: Chain B: W.39 Ligand excluded by PLIP

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