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

Crystal structure of S. aureus FabI in complex with NADP and 5-fluoro- 2-phenoxyphenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 29 residues within 4Å: Chain A: G.39, I.40, A.41, S.45, I.46, R.66, K.67, S.70, I.91, D.92, V.93, S.119, I.120, A.121, F.122, I.146, T.171, T.172, Y.173, K.190, A.216, G.217, P.218, I.219, T.221, L.222, S.223, F.230 Ligands: FPL.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.46, A:Y.173, A:A.216 Hydrogen bonds: A:G.39, A:I.46, A:R.66, A:R.66, A:K.67, A:S.70, A:S.70, A:D.92, A:V.93, A:I.120, A:A.121, A:K.190, A:I.219, A:I.219, A:T.221, A:S.223 Water bridges: A:S.119, A:S.119, A:T.171 Salt bridges: A:R.66, A:K.67 NAP.4: 30 residues within 4Å: Chain B: G.39, I.40, A.41, S.45, I.46, R.66, K.67, S.70, I.91, D.92, V.93, Q.94, S.119, I.120, A.121, F.122, I.146, T.171, T.172, Y.173, K.190, A.216, G.217, P.218, I.219, T.221, L.222, S.223, F.230 Ligands: FPL.5 24 PLIP interactions: 24 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:K.67, B:S.70, B:S.70, B:D.92, B:V.93, B:I.120, B:A.121, B:K.190, B:I.219, B:I.219, B:S.223, B:S.223 Water bridges: B:N.42, B:S.119, B:I.120 Salt bridges: B:R.66, B:K.67 NAP.6: 28 residues within 4Å: Chain C: G.39, I.40, A.41, S.45, I.46, R.66, K.67, 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, F.230 Ligands: FPL.7 27 PLIP interactions: 27 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:K.67, C:S.70, C:S.70, C:D.92, C:V.93, C:I.120, C:A.121, C:K.190, C:I.219, C:I.219, C:T.221, C:S.223, C:S.223 Water bridges: C:S.119, C:S.119, C:T.171, C:L.222 Salt bridges: C:R.66, C:K.67 pi-Cation interactions: C:R.66 NAP.9: 28 residues within 4Å: Chain D: G.39, I.40, A.41, S.45, I.46, R.66, K.67, 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, F.230 Ligands: FPL.10 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:I.46, D:Y.173, D:Y.173, D:A.216 Hydrogen bonds: D:G.39, D:I.46, D:R.66, D:R.66, D:K.67, D:S.70, D:S.70, D:D.92, D:V.93, D:I.120, D:A.121, D:K.190, D:I.219, D:I.219, D:S.223, D:S.223 Water bridges: D:S.119, D:S.119, D:L.222 Salt bridges: D:R.66, D:K.67

4 x FPL: 5-fluoro-2-phenoxyphenol(Non-covalent)

FPL.2: 12 residues within 4Å: Chain A: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, S.223, A.224, V.227, F.230 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.121, A:L.128, A:Y.183, A:A.224, A:V.227, A:F.230 Hydrogen bonds: A:Y.183 pi-Stacking: A:Y.173 FPL.5: 11 residues within 4Å: Chain B: A.121, F.122, A.123, Y.173, Y.183, M.186, K.190, S.223, A.224, F.230 Ligands: NAP.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.121, B:Y.183, B:F.230 Hydrogen bonds: B:Y.183, B:Y.183 pi-Stacking: B:Y.173 FPL.7: 12 residues within 4Å: Chain C: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, S.223, A.224, V.227, F.230 Ligands: NAP.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.121, C:L.128, C:Y.183, C:A.224, C:V.227, C:F.230 Hydrogen bonds: C:Y.183 pi-Stacking: C:Y.173 FPL.10: 12 residues within 4Å: Chain D: A.121, F.122, L.128, Y.173, Y.183, M.186, K.190, S.223, A.224, V.227, F.230 Ligands: NAP.9 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.121, D:L.128, D:Y.183, D:A.224, D:V.227, D:F.230 Hydrogen bonds: D:Y.183, D:Y.183, D:K.190 pi-Stacking: D:Y.173

3 x GLU: GLUTAMIC ACID(Non-functional Binders)(Non-covalent)

GLU.3: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 Ligand-Ligand interactions Water bridges: E.3, E.3 GLU.8: 5 residues within 4Å: Chain C: R.129, G.228, G.229, F.230, N.231 6 PLIP interactions: 6 interactions with chain C, Hydrogen bonds: C:R.129, C:N.231 Water bridges: C:G.229, C:G.229, C:N.231 Salt bridges: C:R.129 GLU.11: 4 residues within 4Å: Chain B: R.129, G.229, N.231, T.232 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:N.231, B:N.231, B:T.232, E.11, E.11 Salt bridges: B:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, A. et al., Rational Optimization of Drug-Target Residence Time: Insights from Inhibitor Binding to the S. Aureus Fabi Enzyme-Product Complex. Biochemistry (2013)

Release Date

2013-06-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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