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

Crystal structure of S. aureus FabI in complex with NADP and 2- phenoxy-5-(2-propenyl)phenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 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: W1G.2 27 PLIP interactions: 27 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:S.223 Water bridges: A:K.67, A:K.67, A:S.119, A:S.119, A:I.120, A:L.222, A:S.223 Salt bridges: A:R.66, A:K.67 NAP.5: 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: W1G.6 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: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, B:S.223 Water bridges: B:N.42, B:A.47, B:S.119, B:T.171, B:S.223 Salt bridges: B:R.66, B:K.67 NAP.8: 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, 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 Ligands: W1G.9 28 PLIP interactions: 28 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:S.70, C:D.92, 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:A.47, C:R.66, C:S.119, C:I.120, C:L.222 Salt bridges: C:R.66, C:K.67 NAP.11: 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: W1G.12 29 PLIP interactions: 29 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:T.221, D:S.223, D:S.223 Water bridges: D:R.66, D:R.66, D:S.119, D:S.119, D:T.171, D:L.222 Salt bridges: D:R.66, D:K.67

4 x W1G: 2-PHENOXY-5-(2-PROPENYL)PHENOL(Non-covalent)

W1G.2: 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.1 12 PLIP interactions: 12 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:Y.183, A:A.224, A:V.227, A:V.227 Hydrogen bonds: A:Y.183 pi-Stacking: A:Y.173 W1G.6: 13 residues within 4Å: Chain B: 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.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.121, B:L.128, B:Y.173, B:Y.173, B:Y.173, B:Y.183, B:Y.183, B:A.224, B:V.227, B:V.227, B:F.230 W1G.9: 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.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.128, C:Y.173, C:Y.173, C:Y.173, C:Y.183, C:Y.183, C:A.224, C:V.227, C:V.227 Hydrogen bonds: C:Y.183 W1G.12: 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.11 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.121, D:L.128, D:Y.173, D:Y.173, D:Y.173, D:Y.183, D:Y.183, D:A.224, D:V.227, D:V.227, D:F.230, D:I.233

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.3: 10 residues within 4Å: Chain A: K.33, Y.35, D.114, G.166, S.167, N.208, R.210, L.260, S.261, S.265 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Y.35, A:D.114 Water bridges: A:K.33, A:D.262, E.3, E.3 Salt bridges: A:K.33, A:R.210 GLU.4: 8 residues within 4Å: Chain A: R.129, A.224, K.225, V.227, G.228, G.229, F.230, N.231 5 PLIP interactions: 5 interactions with chain A, Hydrogen bonds: A:K.225, A:G.229, A:F.230, A:N.231 Salt bridges: A:R.129 GLU.7: 6 residues within 4Å: Chain B: R.129, A.224, K.225, V.227, G.229, F.230 5 PLIP interactions: 5 interactions with chain B, Hydrogen bonds: B:K.225, B:G.229, B:F.230 Water bridges: B:N.231 Salt bridges: B:R.129 GLU.10: 6 residues within 4Å: Chain C: R.129, V.227, G.228, G.229, F.230, N.231 8 PLIP interactions: 4 interactions with chain C, 4 Ligand-Ligand interactions Hydrogen bonds: C:G.229, C:F.230, C:N.231, E.10, E.10, E.10, E.10 Salt bridges: C: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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