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

Crystal structure of S. aureus FabI in complex with NADP and 2-(2- aminophenoxy)-5-hexylphenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

5 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 2 residues within 4Å: Chain A: R.129, G.229 4 PLIP interactions: 4 interactions with chain A, Hydrogen bonds: A:G.229 Water bridges: A:N.231, A:N.231 Salt bridges: A:R.129 GLU.2: 1 residues within 4Å: Chain A: K.225 2 PLIP interactions: 2 interactions with chain A, Hydrophobic interactions: A:K.225 Salt bridges: A:K.225 GLU.5: 4 residues within 4Å: Chain B: R.129, V.227, G.228, G.229 5 PLIP interactions: 5 interactions with chain B, Hydrogen bonds: B:R.129, B:G.229 Water bridges: B:N.182, B:N.231 Salt bridges: B:R.129 GLU.6: 9 residues within 4Å: Chain B: K.33, Y.35, D.114, G.166, N.208, R.210, L.260, S.261, D.262 10 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:Y.35, B:G.166, B:N.208, B:N.208, B:S.261, E.6, E.6 Water bridges: B:D.262 Salt bridges: B:K.33, B:R.210 GLU.9: 3 residues within 4Å: Chain C: R.129, G.228, G.229 3 PLIP interactions: 3 interactions with chain C, Hydrogen bonds: C:R.129, C:G.229 Salt bridges: C:R.129

4 x P1F: 2-(2-azanylphenoxy)-5-hexyl-phenol(Non-covalent)

P1F.3: 18 residues within 4Å: Chain A: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, N.182, Y.183, M.186, K.190, S.223, A.224, V.227, G.228, F.230, I.233 Ligands: NAP.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.128, A:Y.173, A:Y.173, A:Y.173, A:V.180, A:N.182, A:Y.183, A:A.224, A:V.227, A:V.227, A:F.230, A:I.233 Hydrogen bonds: A:A.121, A:Y.183, A:Y.183, A:S.223 P1F.7: 16 residues within 4Å: Chain B: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, Y.183, M.186, K.190, S.223, A.224, V.227, G.228, I.233 Ligands: NAP.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.128, B:V.180, B:Y.183, B:A.224, B:V.227, B:I.233 Hydrogen bonds: B:A.121, B:Y.183, B:S.223 P1F.10: 16 residues within 4Å: Chain C: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, N.182, Y.183, M.186, K.190, S.223, A.224, V.227, G.228 Ligands: NAP.11 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:A.121, C:L.128, C:V.180, C:N.182, C:Y.183, C:A.224, C:V.227, C:V.227 Hydrogen bonds: C:A.121, C:Y.183, C:Y.183, C:S.223 P1F.12: 16 residues within 4Å: Chain D: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, Y.183, M.186, K.190, S.223, A.224, V.227, G.228, I.233 Ligands: NAP.13 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.128, D:Y.173, D:Y.173, D:V.180, D:Y.183, D:A.224, D:V.227, D:I.233 Hydrogen bonds: D:A.121, D:Y.183, D:S.223

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

NAP.4: 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: P1F.3 25 PLIP interactions: 25 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, A:S.223 Water bridges: A:N.42, A:S.119, A:S.119, A:I.120 Salt bridges: A:R.66, A:K.67 NAP.8: 29 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, 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: P1F.7 25 PLIP interactions: 25 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 Water bridges: B:A.47, B:S.119, B:T.171, B:S.223 Salt bridges: B:R.66, B:K.67 NAP.11: 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, S.223, F.230 Ligands: P1F.10 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 Water bridges: C:A.47, C:R.66, C:R.66, C:S.119, C:I.120, C:L.222, C:S.223 Salt bridges: C:R.66, C:K.67 NAP.13: 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: P1F.12 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: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:S.119, D:S.119, D:T.171, 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
A

B
B

C
C

D
D

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

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