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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x MJ5: 5-methyl-2-phenoxyphenol(Non-covalent)

MJ5.1: 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, F.230 Ligands: NAP.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.121, A:L.128, A:Y.173, A:Y.173, A:Y.183, A:A.224, A:V.227, A:F.230 Hydrogen bonds: A:Y.183, A:Y.183 pi-Stacking: A:Y.173 MJ5.5: 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.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.121, B:Y.173, B:Y.183, B:V.227 Hydrogen bonds: B:Y.183 pi-Stacking: B:Y.173 MJ5.8: 13 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 Ligands: NAP.10 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.121, C:L.128, C:Y.173, C:Y.183 Hydrogen bonds: C:Y.183, C:Y.183 pi-Stacking: C:Y.173 MJ5.12: 12 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 Ligands: NAP.13 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.121, D:L.128, D:Y.173, D:Y.183, D:A.224, D:V.227, D:V.227 Hydrogen bonds: D:Y.183 pi-Stacking: D:Y.173

5 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 5 residues within 4Å: Chain A: R.129, K.225, V.227, G.229, F.230 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:K.225, A:G.229, A:F.230 Water bridges: A:N.231, E.2 Salt bridges: A:R.129 GLU.4: 9 residues within 4Å: Chain A: D.114, G.165, G.166, S.167, N.208, R.210, L.260, D.262, S.265 5 PLIP interactions: 5 interactions with chain A, Hydrogen bonds: A:D.114, A:G.166, A:L.260, A:D.262 Salt bridges: A:R.210 GLU.6: 8 residues within 4Å: Chain B: R.129, A.224, K.225, V.227, G.228, G.229, F.230, N.231 11 PLIP interactions: 6 Ligand-Ligand interactions, 5 interactions with chain B Hydrogen bonds: E.6, E.6, E.6, E.6, E.6, E.6, B:R.129, B:G.229, B:F.230, B:N.231 Salt bridges: B:R.129 GLU.9: 7 residues within 4Å: Chain C: R.129, A.224, K.225, V.227, G.228, G.229, F.230 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: E.9, E.9, C:G.229 Salt bridges: C:R.129 GLU.11: 8 residues within 4Å: Chain C: K.33, D.114, G.165, G.166, N.208, R.210, L.260, S.265 5 PLIP interactions: 5 interactions with chain C, Hydrogen bonds: C:D.114, C:G.166, C:L.260 Salt bridges: C:K.33, C:R.210

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

NAP.3: 30 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, 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: MJ5.1 24 PLIP interactions: 24 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: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:S.223 Water bridges: A:S.119, A:S.119, A:I.120, A:L.222 Salt bridges: A:R.66, A:K.67 NAP.7: 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: MJ5.5 27 PLIP interactions: 27 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: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:T.221, B:S.223 Water bridges: B:G.39, B:N.42, B:A.47, B:K.67, B:S.119, B:T.171, B:S.223 Salt bridges: B:R.66, B:K.67 NAP.10: 29 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, 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, F.230 Ligands: MJ5.8 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: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:S.223, C:S.223 Water bridges: C:N.42, C:R.66, C:S.119, C:S.119, C:I.120 Salt bridges: C:R.66, C:K.67 NAP.13: 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, 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, F.230 Ligands: MJ5.12 27 PLIP interactions: 27 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:S.119, D:A.121, D:K.190, D:I.219, D:I.219, D:T.221, D:S.223, D:S.223 Water bridges: D:N.42, D:S.119, D:I.120, D:S.223 Salt bridges: D:R.66, D:K.67

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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