SMTL ID : 4cv1.1 (1 other biounit)

Crystal structure of S. aureus FabI in complex with NADPH and CG400549

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: V.227, G.228, G.229, F.230, N.231, T.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.229, A:N.231 SO4.15: 6 residues within 4Å: Chain D: V.227, G.228, G.229, F.230, N.231, T.232 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:V.227, D:G.229, D:F.230, D:N.231, D:N.231, D:T.232, D:T.232 Water bridges: D:R.129

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

NDP.2: 26 residues within 4Å: Chain A: G.39, I.40, A.41, S.45, I.46, R.66, K.67, 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, S.223 Ligands: PT6.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.46, A:Y.173, A:A.216 Hydrogen bonds: A:G.39, A:S.45, A:I.46, A:D.92, A:V.93, A:I.120, A:A.121, A:K.190, A:I.219, A:I.219, A:T.221, A:T.221, A:S.223, A:S.223 Water bridges: A:N.42, A:N.42, A:R.66, A:R.66, A:S.70, A:S.119, A:S.119, A:T.171 Salt bridges: A:R.66, A:K.67 pi-Cation interactions: A:R.66 NDP.5: 27 residues within 4Å: Chain B: G.39, I.40, A.41, S.45, I.46, R.66, K.67, 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, S.223, F.230 Ligands: PT6.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.46, B:Y.173, B:Y.173, B:A.216 Hydrogen bonds: B:G.39, B:S.45, B:I.46, B:D.92, B:D.92, B:V.93, B:Q.94, B:I.120, B:K.190, B:I.219, B:I.219, B:T.221, B:S.223, B:S.223 Water bridges: B:G.39, B:R.66, B:R.66, B:S.119, B:I.120 Salt bridges: B:R.66, B:K.67 pi-Cation interactions: B:R.66 NDP.9: 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, 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, S.223, F.230 Ligands: PT6.10 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:I.46, C:Y.173, C:A.216 Hydrogen bonds: C:G.39, C:S.45, C:I.46, 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:T.221, C:S.223 Water bridges: C:A.47, C:S.119, C:I.120, C:L.222 Salt bridges: C:R.66, C:K.67 pi-Cation interactions: C:R.66 NDP.13: 27 residues within 4Å: Chain D: G.39, I.40, A.41, S.45, I.46, R.66, K.67, 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, S.223, F.230 Ligands: PT6.14 23 PLIP interactions: 23 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:D.92, D:V.93, D:Q.94, D:S.119, D:A.121, D:K.190, D:I.219, D:I.219, D:T.221, D:S.223 Water bridges: D:N.42, D:A.47, D:T.171 Salt bridges: D:R.66, D:K.67 pi-Cation interactions: D:R.66

4 x PT6: 1-(3-amino-2-methylbenzyl)-4-[2-(thiophen-2-yl)ethoxy]pyridin-2(1H)-one(Non-covalent)

PT6.3: 13 residues within 4Å: Chain A: A.121, F.122, A.123, M.125, Y.173, V.180, Q.181, Y.183, M.186, S.223, V.227, F.230 Ligands: NDP.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.173, A:V.180, A:Y.183, A:Y.183, A:F.230 Hydrogen bonds: A:A.123, A:A.123 pi-Stacking: A:Y.183 PT6.6: 18 residues within 4Å: Chain B: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, Y.183, M.186, P.218, S.223, A.224, V.227, G.228, G.229, F.230, I.233 Ligands: NDP.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.128, B:Y.173, B:V.180, B:Y.183, B:Y.183, B:P.218, B:A.224, B:V.227 Hydrogen bonds: B:A.123, B:A.123, B:Y.183 pi-Stacking: B:Y.183 PT6.10: 18 residues within 4Å: Chain C: A.121, F.122, A.123, M.125, L.128, Y.173, V.180, Q.181, Y.183, M.186, P.218, S.223, A.224, V.227, G.228, F.230, I.233 Ligands: NDP.9 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.128, C:Y.173, C:V.180, C:Y.183, C:Y.183, C:P.218, C:A.224, C:I.233 Hydrogen bonds: C:A.123, C:A.123, C:Y.183 pi-Stacking: C:Y.183 PT6.14: 18 residues within 4Å: Chain D: A.121, F.122, A.123, L.128, Y.173, V.180, Q.181, Y.183, M.186, P.218, S.223, A.224, V.227, G.228, G.229, F.230, I.233 Ligands: NDP.13 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.128, D:Y.173, D:V.180, D:Y.183, D:P.218, D:A.224, D:I.233 Hydrogen bonds: D:A.123, D:A.123

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: K.67, E.68, R.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.68, A:R.69 EDO.8: 6 residues within 4Å: Chain C: V.227, G.228, G.229, F.230, N.231, T.232 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.229, C:F.230, C:N.231, C:N.231 EDO.11: 2 residues within 4Å: Chain B: V.53 Chain C: A.26 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain D: G.166, N.208, R.210, D.262 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.208, D:R.210, D:S.261

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain B: R.66, R.69 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiebel, J. et al., Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (Acp) Reductase Inhibitor. J.Biol.Chem. (2014)

Release Date

2014-04-16

Peptides

ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

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

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