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

Crystal structure of S. aureus FabI in complex with NADP and 2- phenoxy-5-propylphenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

3 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 4 residues within 4Å: Chain A: R.129, G.229, F.230, N.231 6 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain A Hydrogen bonds: E.1, E.1, A:G.229, A:F.230, A:N.231 Salt bridges: A:R.129 GLU.4: 6 residues within 4Å: Chain B: R.129, K.225, V.227, G.228, G.229, F.230 8 PLIP interactions: 2 Ligand-Ligand interactions, 6 interactions with chain B Hydrogen bonds: E.4, E.4, B:K.225, B:G.229, B:F.230 Water bridges: B:N.231 Salt bridges: B:R.129, B:R.129 GLU.7: 3 residues within 4Å: Chain C: R.129, G.228, G.229 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain C Water bridges: E.7, C:N.231 Hydrogen bonds: C:V.227, C:G.229 Salt bridges: C:R.129

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

NAP.2: 28 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, 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: PV4.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.46, A:Y.173, 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:D.92, A:D.92, A:V.93, A:I.120, A:A.121, A:K.190, A:I.219, A:I.219, A:S.223, A:S.223 Water bridges: A:A.47, A:S.119, A:T.171 Salt bridges: A:R.66, A:K.67 NAP.5: 28 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, 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: PV4.6 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.46, 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:I.120, B:A.121, B:K.190, B:I.219, B:I.219, B:S.223 Water bridges: B:S.119, B:S.119, B:T.171, B:L.222 Salt bridges: B:R.66, B:K.67 NAP.8: 27 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 Ligands: PV4.9 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:I.46, C:Y.173, C:A.216 Hydrogen bonds: C:G.39, C:I.46, C:R.66, C:R.66, C:K.67, 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 Water bridges: C:N.42, C:A.47, C:T.171, C:L.222 Salt bridges: C:R.66, C:K.67 pi-Cation interactions: C:R.66 NAP.10: 29 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, 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, A.224 Ligands: PV4.11 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:I.46, 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:D.92, D:V.93, D:I.120, D:A.121, D:K.190, D:I.219, D:I.219, D:T.221, D:T.221, D:S.223, D:S.223 Water bridges: D:N.42, D:A.47, D:I.120, D:L.222 Salt bridges: D:R.66, D:K.67

4 x PV4: 2-phenoxy-5-propyl-phenol(Non-covalent)

PV4.3: 13 residues within 4Å: Chain A: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, K.190, S.223, A.224, V.227, I.233 Ligands: NAP.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.121, A:L.128, A:Y.173, A:Y.173, A:Y.173, A:Y.183, A:A.224, A:V.227, A:V.227, A:I.233 Hydrogen bonds: A:Y.183 PV4.6: 12 residues within 4Å: Chain B: A.121, F.122, A.123, Y.173, Y.183, M.186, K.190, S.223, A.224, V.227, F.230 Ligands: NAP.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.121, B:Y.173, B:Y.183, B:V.227, B:F.230 Hydrogen bonds: B:Y.183 PV4.9: 14 residues within 4Å: Chain C: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, K.190, S.223, A.224, V.227, F.230, I.233 Ligands: NAP.8 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, C:F.230, C:I.233 PV4.11: 14 residues within 4Å: Chain D: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, K.190, S.223, A.224, V.227, F.230, I.233 Ligands: NAP.10 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.128, D:Y.173, D:Y.183, D:Y.183, D:A.224, D:V.227, D:F.230, D:I.233 pi-Stacking: D:Y.173

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
E

B
F

C
G

D
H

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

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