SMTL ID : 4cuz.1 (1 other biounit)

Crystal structure of S. aureus FabI in complex with NADPH and PT173

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-tetramer

Ligands

4 x AEW: 1-(3-amino-2-methylbenzyl)-4-hexylpyridin-2(1H)-one(Non-covalent)

AEW.1: 13 residues within 4Å: Chain A: A.121, F.122, A.123, L.128, Y.173, Q.181, N.182, Y.183, M.186, S.223, V.227, F.230 Ligands: NDP.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.128, A:Y.173, A:N.182, A:Y.183, A:Y.183, A:V.227, A:F.230 Hydrogen bonds: A:A.123, A:A.123, A:Y.183 AEW.3: 13 residues within 4Å: Chain B: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, N.182, Y.183, M.186, K.190, S.223 Ligands: NDP.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.128, B:Y.173, B:V.180, B:N.182, B:Y.183 Hydrogen bonds: B:A.123, B:A.123 AEW.6: 12 residues within 4Å: Chain C: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, Y.183, M.186, S.223, F.230 Ligands: NDP.7 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.128, C:Y.173, C:V.180, C:Y.183, C:F.230 Hydrogen bonds: C:A.123, C:A.123 AEW.8: 13 residues within 4Å: Chain D: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, N.182, Y.183, M.186, S.223, F.230 Ligands: NDP.9 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.128, D:Y.173, D:Y.173, D:V.180, D:N.182, D:Y.183, D:F.230 Hydrogen bonds: D:A.123, D:A.123, D:Y.183

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

NDP.2: 25 residues within 4Å: Chain A: G.39, I.40, A.41, S.45, I.46, R.66, S.70, I.91, D.92, V.93, S.119, I.120, A.121, I.146, T.171, T.172, Y.173, K.190, A.216, G.217, P.218, I.219, T.221, S.223 Ligands: AEW.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.46, A:Y.173, A:Y.173, A:A.216 Hydrogen bonds: A:G.39, A:G.39, A:A.41, A:I.46, A:R.66, A:S.70, A:D.92, A:V.93, A:S.119, A:A.121, A:K.190, A:I.219, A:I.219, A:T.221, A:T.221, A:S.223, A:S.223 Salt bridges: A:R.66 pi-Cation interactions: A:R.66 NDP.4: 25 residues within 4Å: Chain B: G.39, I.40, A.41, S.45, I.46, R.66, S.70, I.91, D.92, V.93, S.119, I.120, A.121, I.146, T.171, T.172, Y.173, K.190, A.216, G.217, P.218, I.219, T.221, S.223 Ligands: AEW.3 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.46, B:Y.173, B:Y.173, B:A.216 Hydrogen bonds: B:G.39, B:I.46, B:R.66, B:R.66, B:K.67, B:S.70, B:D.92, B:V.93, B:S.119, B:A.121, B:K.190, B:I.219, B:I.219, B:T.221, B:S.223, B:S.223 Salt bridges: B:R.66 pi-Cation interactions: B:R.66 NDP.7: 27 residues within 4Å: Chain C: G.39, I.40, A.41, N.42, S.45, I.46, R.66, S.70, I.91, D.92, V.93, S.119, I.120, A.121, I.146, T.171, T.172, Y.173, K.190, A.216, G.217, P.218, I.219, T.221, L.222, S.223 Ligands: AEW.6 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:I.46, C:Y.173, C:Y.173, C:A.216 Hydrogen bonds: C:G.39, C:I.46, C:R.66, C:S.70, C:D.92, C:V.93, C:S.119, C:S.119, C:K.190, C:I.219, C:I.219, C:T.221, C:T.221, C:L.222, C:S.223, C:S.223 Salt bridges: C:R.66 pi-Cation interactions: C:R.66 NDP.9: 25 residues within 4Å: Chain D: G.39, I.40, A.41, S.45, I.46, R.66, S.70, I.91, D.92, V.93, S.119, I.120, A.121, I.146, T.171, T.172, Y.173, K.190, A.216, G.217, P.218, I.219, T.221, S.223 Ligands: AEW.8 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Y.173, D:Y.173 Hydrogen bonds: D:G.39, D:A.41, D:I.46, D:R.66, D:S.70, D:D.92, D:V.93, D:S.119, D:S.119, D:A.121, D:K.190, D:I.219, D:I.219, D:T.221, D:S.223, D:S.223 Salt bridges: D:R.66 pi-Cation interactions: D:R.66

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain C: V.227, G.228, G.229, F.230, N.231, T.232 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:V.227, C:G.229, C:F.230, C:N.231, C:N.231, C:T.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiebel, J. et al., Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (Acp) Reductase Inhibitor. J.Biol.Chem. (2014)

Release Date

2014-04-16

Peptides

ENOYL-ACP REDUCTASE MOLECULE ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ENOYL-ACP REDUCTASE MOLECULE ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]

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