SMTL ID : 4xjm.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a HTS lead compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x 41E: 3-{1-[(5-acetylthiophen-2-yl)carbonyl]piperidin-4-yl}-N-(3-methoxyphenyl)propanamide(Non-covalent)

41E.1: 18 residues within 4Å: Chain A: P.44, Y.45, W.84, Y.177, M.185, G.192, G.193, M.194, W.198, A.246 Chain B: M.111, F.112, G.113, K.153, M.334, G.336, P.337, T.338 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:M.334, A:P.44, A:Y.45, A:W.84, A:Y.177, A:Y.177, A:M.194, A:A.246 Hydrogen bonds: B:F.112, B:G.113, A:Y.45 pi-Stacking: A:W.84, A:W.84 41E.3: 19 residues within 4Å: Chain A: M.111, F.112, G.113, K.153, M.334, G.336, P.337, T.338 Chain B: P.44, Y.45, W.84, Y.177, M.185, G.192, G.193, M.194, W.198, A.246, F.422 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.44, B:Y.45, B:W.84, B:M.194, B:A.246, B:F.422, A:M.334 Hydrogen bonds: B:Y.45, B:Y.45, A:F.112, A:G.113 pi-Stacking: B:W.84, B:W.84

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

PLP.2: 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 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.177, A:E.240, A:I.276 Hydrogen bonds: A:G.144, A:S.145, B:T.338, B:T.338 Water bridges: A:S.143, A:S.145, A:S.145, A:D.180, A:E.240 Salt bridges: A:K.303 pi-Stacking: A:Y.177 PLP.4: 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 14 PLIP interactions: 11 interactions with chain B, 3 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, A:T.338, A:T.338, A:T.338 Water bridges: B:S.145, B:Y.177, B:D.180, B:E.240 pi-Stacking: B:Y.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Finzel, B.C. et al., Fragment based inhibitor design of Mycobacterium tuberculosis BioA (http://hdl.handle.net/11299/171084). Thesis, University of Minnesota (2015)

Release Date

2016-01-20

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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