SMTL ID : 6tbc.2 (1 other biounit)

Crystal structure of S. aureus FabI in complex with NADPH and kalimantacin B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 28 residues within 4Å: Chain A: G.18, I.19, A.20, S.24, I.25, R.45, K.46, S.49, I.70, D.71, V.72, Q.73, S.98, I.99, A.100, I.125, T.150, T.151, Y.152, K.169, A.195, G.196, P.197, I.198, T.200, L.201, S.202 Ligands: N5H.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.25, A:Y.152, A:A.195 Hydrogen bonds: A:G.18, A:G.18, A:I.25, A:R.45, A:R.45, A:K.46, A:S.49, A:S.49, A:D.71, A:V.72, A:Q.73, A:I.99, A:A.100, A:K.169, A:I.198, A:I.198, A:L.201, A:S.202, A:S.202 Salt bridges: A:R.45, A:K.46 NDP.3: 28 residues within 4Å: Chain B: G.18, I.19, A.20, S.24, I.25, R.45, K.46, S.49, I.70, D.71, V.72, Q.73, S.98, I.99, A.100, I.125, T.150, T.151, Y.152, K.169, A.195, G.196, P.197, I.198, T.200, L.201, S.202 Ligands: N5H.4 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.25, B:Y.152, B:A.195 Hydrogen bonds: B:G.18, B:S.24, B:I.25, B:R.45, B:R.45, B:K.46, B:S.49, B:D.71, B:V.72, B:Q.73, B:I.99, B:A.100, B:Y.162, B:K.169, B:I.198, B:I.198, B:T.200, B:S.202, B:S.202 Salt bridges: B:R.45 NDP.5: 28 residues within 4Å: Chain C: G.18, I.19, A.20, S.24, I.25, R.45, K.46, S.49, I.70, D.71, V.72, Q.73, S.98, I.99, A.100, I.125, T.150, T.151, Y.152, K.169, A.195, G.196, P.197, I.198, T.200, L.201, S.202 Ligands: N5H.6 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.25, C:Y.152, C:A.195 Hydrogen bonds: C:G.18, C:I.25, C:R.45, C:R.45, C:K.46, C:S.49, C:S.49, C:D.71, C:V.72, C:Q.73, C:S.98, C:I.99, C:A.100, C:Y.162, C:K.169, C:I.198, C:I.198, C:T.200, C:S.202 Salt bridges: C:R.45 NDP.7: 31 residues within 4Å: Chain D: G.18, I.19, A.20, S.24, I.25, R.45, K.46, R.48, S.49, I.70, D.71, V.72, Q.73, S.98, I.99, A.100, F.101, I.125, T.150, T.151, Y.152, K.169, A.195, G.196, P.197, I.198, T.200, S.202, A.203, F.209 Ligands: N5H.8 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:I.25, D:Y.152, D:A.195 Hydrogen bonds: D:G.18, D:S.24, D:I.25, D:R.45, D:R.45, D:K.46, D:S.49, D:D.71, D:V.72, D:Q.73, D:I.99, D:A.100, D:K.169, D:I.198, D:I.198, D:T.200, D:S.202 Salt bridges: D:R.45, D:R.48

4 x N5H: (2~{E},5~{R},10~{E},12~{E},15~{S},19~{R})-20-[[(2~{R},3~{R})-3-aminocarbonyloxy-2-methyl-butanoyl]amino]-3,5,15-trimethyl-7-methylidene-19-oxidanyl-17-oxidanylidene-icosa-2,10,12-trienoic acid(Non-covalent)

N5H.2: 17 residues within 4Å: Chain A: R.45, A.100, F.101, A.102, M.104, Y.152, V.159, Q.160, Y.162, M.165, L.201, S.202, A.203, V.206, F.209, I.212 Ligands: NDP.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.100, A:Y.152, A:Y.152, A:V.159, A:Y.162, A:Y.162, A:L.201, A:A.203, A:V.206, A:F.209, A:F.209, A:I.212 Hydrogen bonds: A:R.45, A:A.100, A:A.102, A:A.102, A:M.104 Salt bridges: A:K.169 N5H.4: 17 residues within 4Å: Chain B: A.100, F.101, A.102, M.104, L.107, Y.152, V.159, Q.160, N.161, Y.162, M.165, L.201, S.202, A.203, V.206, I.212 Ligands: NDP.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.100, B:L.107, B:V.159, B:Y.162, B:L.201, B:A.203, B:V.206, B:V.206, B:I.212 Hydrogen bonds: B:A.100, B:A.102, B:A.102, B:M.104, B:Y.162 Salt bridges: B:K.169 N5H.6: 16 residues within 4Å: Chain C: A.100, F.101, A.102, M.104, L.107, Y.152, V.159, Q.160, Y.162, M.165, L.201, S.202, A.203, V.206, I.212 Ligands: NDP.5 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.100, C:L.107, C:Y.152, C:V.159, C:Y.162, C:L.201, C:A.203, C:V.206, C:I.212 Hydrogen bonds: C:A.102, C:A.102, C:M.104, C:Y.162, C:S.202 Salt bridges: C:K.169 N5H.8: 17 residues within 4Å: Chain D: R.48, A.100, F.101, A.102, M.104, L.107, Y.152, V.159, Q.160, Y.162, M.165, S.202, A.203, V.206, F.209, I.212 Ligands: NDP.7 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:A.100, D:L.107, D:Y.152, D:V.159, D:Y.162, D:A.203, D:V.206, D:F.209, D:F.209, D:I.212 Hydrogen bonds: D:A.100, D:A.102, D:A.102, D:M.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fage, C.D. et al., The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in Staphylococcus aureus by Targeting the Enoyl-Acyl Carrier Protein Binding Site of FabI. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2020-04-01

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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