SMTL ID : 5i9m.2 (1 other biounit)

Crystal structure of B. pseudomallei FabI in complex with NAD and PT408

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.13, L.14, L.15, S.19, I.20, V.40, C.63, D.64, V.65, S.91, I.92, G.93, F.94, I.119, L.144, S.145, Y.146, M.159, K.163, A.189, G.190, P.191, I.192, T.194, L.195, A.196, F.203 Ligands: 69K.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.20, A:Y.146, A:Y.146 Hydrogen bonds: A:G.13, A:I.20, A:D.64, A:D.64, A:V.65, A:I.92, A:G.93, A:K.163, A:I.192, A:I.192, A:T.194, A:T.194, A:A.196 Water bridges: A:S.91, A:I.92, A:L.195 NAD.3: 28 residues within 4Å: Chain B: G.13, L.14, L.15, S.19, I.20, V.40, C.63, D.64, V.65, S.91, I.92, G.93, F.94, I.119, L.144, S.145, Y.146, M.159, K.163, A.189, G.190, P.191, I.192, T.194, L.195, A.196, F.203 Ligands: 69K.4 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.20, B:Y.146, B:Y.146 Hydrogen bonds: B:G.13, B:I.20, B:D.64, B:D.64, B:V.65, B:I.92, B:G.93, B:K.163, B:I.192, B:I.192, B:T.194, B:T.194, B:A.196 Water bridges: B:G.13, B:S.91, B:I.92, B:L.195 NAD.5: 28 residues within 4Å: Chain C: G.13, L.14, L.15, S.19, I.20, V.40, C.63, D.64, V.65, S.91, I.92, G.93, F.94, I.119, L.144, S.145, Y.146, M.159, K.163, A.189, G.190, P.191, I.192, T.194, L.195, A.196, F.203 Ligands: 69K.6 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.20, C:Y.146, C:Y.146 Hydrogen bonds: C:G.13, C:I.20, C:D.64, C:V.65, C:I.92, C:G.93, C:K.163, C:I.192, C:I.192, C:T.194, C:A.196 Water bridges: C:G.13, C:S.91, C:I.92, C:L.195 NAD.7: 28 residues within 4Å: Chain D: G.13, L.14, L.15, S.19, I.20, V.40, C.63, D.64, V.65, S.91, I.92, G.93, F.94, I.119, L.144, S.145, Y.146, M.159, K.163, A.189, G.190, P.191, I.192, T.194, L.195, A.196, F.203 Ligands: 69K.8 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.20, D:Y.146, D:Y.146 Hydrogen bonds: D:G.13, D:I.20, D:D.64, D:V.65, D:I.92, D:G.93, D:K.163, D:I.192, D:I.192, D:T.194, D:A.196 Water bridges: D:G.13, D:S.91, D:I.92, D:L.195

4 x 69K: 5-ethyl-4-fluoro-2-[(2-methylpyridin-3-yl)oxy]phenol(Non-covalent)

69K.2: 13 residues within 4Å: Chain A: G.93, F.94, A.95, I.100, Y.146, Y.156, M.159, K.163, A.196, A.197, I.200, F.203 Ligands: NAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.100, A:Y.146, A:Y.146, A:Y.146, A:Y.156, A:A.196, A:I.200 Hydrogen bonds: A:A.95, A:Y.156, A:K.163, A:K.163 pi-Stacking: A:Y.146 69K.4: 13 residues within 4Å: Chain B: G.93, F.94, A.95, I.100, Y.146, Y.156, M.159, K.163, A.196, A.197, I.200, F.203 Ligands: NAD.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.100, B:Y.146, B:Y.146, B:Y.146, B:Y.156, B:A.196, B:I.200 Hydrogen bonds: B:A.95, B:Y.156, B:K.163, B:K.163 pi-Stacking: B:Y.146 69K.6: 13 residues within 4Å: Chain C: G.93, F.94, A.95, I.100, Y.146, Y.156, M.159, K.163, A.196, A.197, I.200, F.203 Ligands: NAD.5 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.100, C:Y.146, C:Y.146, C:Y.146, C:Y.156, C:A.196, C:I.200 Hydrogen bonds: C:A.95, C:K.163, C:K.163 pi-Stacking: C:Y.146 69K.8: 13 residues within 4Å: Chain D: G.93, F.94, A.95, I.100, Y.146, Y.156, M.159, K.163, A.196, A.197, I.200, F.203 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.100, D:Y.146, D:Y.146, D:Y.146, D:Y.156, D:A.196, D:I.200 Hydrogen bonds: D:A.95, D:K.163, D:K.163 pi-Stacking: D:Y.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neckles, C. et al., Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase. Biochemistry (2017)

Release Date

2017-02-22

Peptides

Enoyl-[acyl-carrier-protein] reductase [NADH]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
C

D
C

Enoyl-[acyl-carrier-protein] reductase [NADH]

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