SMTL ID : 6t5x.1

Crystal structure of Salmonella typhimurium FabG in complex with NADPH at 1.5 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 28 residues within 4Å: Chain A: G.12, A.13, S.14, R.15, G.16, I.17, A.36, T.37, L.58, N.59, V.60, N.86, A.87, G.88, I.89, T.109, I.136, G.137, S.138, Y.151, K.155, P.181, G.182, F.183, I.184, T.186, M.188, T.189 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:P.181 Hydrogen bonds: A:G.12, A:S.14, A:S.14, A:S.14, A:I.17, A:T.37, A:T.37, A:N.59, A:V.60, A:N.86, A:G.88, A:Y.151, A:K.155, A:I.184, A:I.184, A:T.186, A:T.186 Water bridges: A:G.12, A:R.15, A:R.15, A:T.37, A:T.37, A:N.86, A:T.109 Salt bridges: A:R.15, A:R.15 NDP.5: 23 residues within 4Å: Chain B: G.12, S.14, R.15, I.17, A.36, T.37, L.58, N.59, V.60, N.86, A.87, G.88, I.89, T.109, I.136, G.137, Y.151, K.155, P.181, G.182, I.184, T.186 Ligands: GOL.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:P.181 Hydrogen bonds: B:G.12, B:S.14, B:S.14, B:T.37, B:T.37, B:N.59, B:V.60, B:N.86, B:G.88, B:Y.151, B:K.155, B:G.182, B:I.184 Water bridges: B:G.12, B:R.15, B:R.15, B:T.37, B:T.37, B:N.86, B:G.88, B:G.88, B:I.89, B:T.186 Salt bridges: B:R.15, B:R.15 NDP.7: 28 residues within 4Å: Chain C: G.12, A.13, S.14, R.15, G.16, I.17, A.36, T.37, L.58, N.59, V.60, N.86, A.87, G.88, I.89, T.109, I.136, G.137, S.138, Y.151, K.155, P.181, G.182, F.183, I.184, T.186, M.188, T.189 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:P.181 Hydrogen bonds: C:G.12, C:S.14, C:S.14, C:S.14, C:I.17, C:T.37, C:T.37, C:N.59, C:V.60, C:N.86, C:G.88, C:K.155, C:I.184, C:I.184, C:T.186 Water bridges: C:G.12, C:R.15, C:R.15, C:T.37, C:T.37, C:S.38, C:N.86, C:N.86 Salt bridges: C:R.15, C:R.15 NDP.11: 23 residues within 4Å: Chain D: G.12, S.14, R.15, I.17, A.36, T.37, L.58, N.59, V.60, N.86, A.87, G.88, I.89, T.109, I.136, G.137, Y.151, K.155, P.181, G.182, I.184, T.186 Ligands: GOL.12 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:P.181 Hydrogen bonds: D:G.12, D:S.14, D:S.14, D:T.37, D:T.37, D:N.59, D:V.60, D:N.86, D:G.88, D:K.155, D:G.182, D:I.184 Water bridges: D:G.12, D:R.15, D:R.15, D:S.38, D:N.86, D:G.88, D:G.88, D:I.89, D:T.186, D:T.186 Salt bridges: D:R.15, D:R.15

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: E.233, T.234 Chain B: E.233, T.234 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.234 NA.8: 4 residues within 4Å: Chain C: E.233, T.234 Chain D: E.233, T.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.234

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: I.89, R.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.91, A:R.91 GOL.4: 3 residues within 4Å: Chain A: S.2, D.225, E.226 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.2 Water bridges: A:S.2, A:S.224, A:D.225 GOL.6: 3 residues within 4Å: Chain B: I.89, R.91 Ligands: NDP.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.91, B:R.91 Water bridges: B:T.90 GOL.9: 2 residues within 4Å: Chain C: I.89, R.91 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.91, C:R.91 GOL.10: 3 residues within 4Å: Chain C: S.2, D.225, E.226 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.2, C:E.226 Water bridges: C:S.2, C:S.224, C:D.225 GOL.12: 3 residues within 4Å: Chain D: I.89, R.91 Ligands: NDP.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.91, D:R.91 Water bridges: D:T.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vella, P. et al., A FabG inhibitor targeting an allosteric binding site inhibits several orthologs from Gram-negative ESKAPE pathogens. Bioorg.Med.Chem. (2021)

Release Date

2020-11-18

Peptides

3-oxoacyl-[acyl-carrier-protein] reductase FabG: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

3-oxoacyl-[acyl-carrier-protein] reductase FabG