SMTL ID : 4xjl.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 1.85 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 8 residues within 4Å: Chain A: R.213, D.214, V.242, H.252, D.253, P.254, H.291, C.391 No protein-ligand interaction detected (PLIP)

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

PLP.2: 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 13 PLIP interactions: 11 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 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 15 PLIP interactions: 12 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.143, B:Y.177, B:D.180, B:E.240 Salt bridges: B:K.303 pi-Stacking: B:Y.177

2 x 41F: N-(1,2,3-benzothiadiazol-5-yl)-4-phenylpiperazine-1-carboxamide(Non-covalent)

41F.3: 16 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, C.188, D.189, G.192, G.193, A.246 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.44, B:Y.177 pi-Stacking: B:W.84, B:W.84, B:W.84 Hydrogen bonds: A:F.112 41F.4: 15 residues within 4Å: Chain A: P.44, Y.45, W.84, Y.177, C.188, D.189, G.192, G.193, A.246 Chain B: M.111, F.112, G.113, G.336, P.337, T.338 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:F.112, B:G.113 Hydrophobic interactions: A:P.44, A:Y.177 pi-Stacking: A:W.84, A:W.84, A:W.84

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

PEG.5: 6 residues within 4Å: Chain B: R.213, V.242, H.252, D.253, P.254, H.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, R., 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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