SMTL ID : 5i8z.1

Crystal structure of B. pseudomallei FabI in complex with NAD and PT12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: G.13, 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, K.163, A.189, G.190, P.191, I.192, T.194, L.195, A.196 Ligands: JA1.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.20, A:Y.146, A:A.189 Hydrogen bonds: A:G.13, A:S.19, A:I.20, 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:A.196 Water bridges: A:V.40, A:V.40, A:S.91, A:S.91, A:I.92, A:L.195, A:L.195 NAD.3: 25 residues within 4Å: Chain B: G.13, 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, K.163, A.189, G.190, P.191, I.192, T.194, L.195, A.196 Ligands: JA1.4 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.20, B:Y.146, B:A.189 Hydrogen bonds: B:G.13, B:S.19, B:I.20, 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:A.196 Water bridges: B:G.13, B:V.40, B:V.40, B:S.91, B:S.91, B:I.92, B:L.195, B:L.195 NAD.5: 25 residues within 4Å: Chain C: G.13, 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, K.163, A.189, G.190, P.191, I.192, T.194, L.195, A.196 Ligands: JA1.6 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.20, C:Y.146, C:A.189 Hydrogen bonds: C:G.13, C:S.19, C:I.20, C:D.64, C:D.64, C:V.65, C:I.92, C:G.93, C:K.163, C:I.192, C:I.192, C:A.196 Water bridges: C:G.13, C:V.40, C:V.40, C:S.91, C:S.91, C:I.92, C:L.195, C:L.195 NAD.7: 25 residues within 4Å: Chain D: G.13, 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, K.163, A.189, G.190, P.191, I.192, T.194, L.195, A.196 Ligands: JA1.8 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.20, D:Y.146, D:A.189 Hydrogen bonds: D:G.13, D:S.19, D:I.20, D:D.64, D:D.64, D:V.65, D:I.92, D:G.93, D:K.163, D:I.192, D:I.192, D:A.196 Water bridges: D:G.13, D:V.40, D:V.40, D:S.91, D:S.91, D:I.92, D:L.195, D:L.195

4 x JA1: 5-HEXYL-2-(4-NITROPHENOXY)PHENOL(Non-covalent)

JA1.2: 13 residues within 4Å: Chain A: G.93, F.94, A.95, I.100, Y.146, P.154, N.155, Y.156, K.163, A.196, I.200, F.203 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.146, A:Y.146, A:Y.146, A:N.155, A:Y.156, A:Y.156, A:A.196, A:I.200, A:F.203 Hydrogen bonds: A:A.95 JA1.4: 13 residues within 4Å: Chain B: G.93, F.94, A.95, I.100, Y.146, P.154, N.155, Y.156, K.163, A.196, I.200, F.203 Ligands: NAD.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.146, B:Y.146, B:Y.146, B:N.155, B:Y.156, B:Y.156, B:A.196, B:I.200, B:F.203 Hydrogen bonds: B:A.95 JA1.6: 13 residues within 4Å: Chain C: G.93, F.94, A.95, I.100, Y.146, P.154, N.155, Y.156, K.163, A.196, I.200, F.203 Ligands: NAD.5 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.146, C:Y.146, C:Y.146, C:N.155, C:Y.156, C:Y.156, C:A.196, C:I.200, C:F.203 Hydrogen bonds: C:A.95, C:Y.156 JA1.8: 13 residues within 4Å: Chain D: G.93, F.94, A.95, I.100, Y.146, P.154, N.155, Y.156, K.163, A.196, I.200, F.203 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.146, D:Y.146, D:Y.146, D:N.155, D:Y.156, D:Y.156, D:A.196, D:I.200, D:F.203 Hydrogen bonds: D:A.95, D:Y.156

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
A

B
A

C
A

D
A

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

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