SMTL ID : 3sj7.1

Structure of beta-ketoacetyl-CoA reductase (FabG) from Staphylococcus aureus complex with NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NDP.1: 29 residues within 4Å: Chain A: G.17, A.18, S.19, R.20, G.21, I.22, N.40, Y.41, A.42, G.43, S.44, A.67, N.68, V.69, N.95, A.96, G.97, I.98, T.118, L.145, S.146, S.147, Y.160, K.164, P.190, G.191, I.193, S.195 Ligands: PG4.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.190 Hydrogen bonds: A:G.17, A:S.19, A:S.19, A:I.22, A:A.42, A:G.43, A:S.44, A:N.68, A:V.69, A:N.95, A:G.97, A:Y.160, A:K.164, A:I.193, A:S.195 Water bridges: A:G.23, A:G.23 Salt bridges: A:R.20, A:R.20 NDP.4: 28 residues within 4Å: Chain B: G.17, S.19, R.20, G.21, I.22, N.40, Y.41, A.42, G.43, S.44, A.67, N.68, V.69, N.95, A.96, G.97, I.98, T.118, L.145, S.146, S.147, Y.160, K.164, P.190, G.191, I.193, S.195 Ligands: PG4.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:P.190 Hydrogen bonds: B:G.17, B:S.19, B:S.19, B:I.22, B:A.42, B:G.43, B:S.44, B:N.68, B:V.69, B:N.95, B:G.97, B:Y.160, B:K.164, B:I.193, B:S.195, B:S.195 Water bridges: B:G.97, B:I.98 Salt bridges: B:R.20, B:R.20 NDP.6: 29 residues within 4Å: Chain C: G.17, A.18, S.19, R.20, G.21, I.22, N.40, Y.41, A.42, G.43, S.44, A.67, N.68, V.69, N.95, A.96, G.97, I.98, T.118, L.145, S.146, S.147, Y.160, K.164, P.190, G.191, I.193, S.195 Ligands: PG4.7 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.190 Hydrogen bonds: C:G.17, C:S.19, C:S.19, C:I.22, C:A.42, C:G.43, C:S.44, C:N.68, C:V.69, C:N.95, C:G.97, C:K.164, C:I.193, C:S.195 Water bridges: C:G.23, C:G.23 Salt bridges: C:R.20, C:R.20 NDP.9: 28 residues within 4Å: Chain D: G.17, S.19, R.20, G.21, I.22, N.40, Y.41, A.42, G.43, S.44, A.67, N.68, V.69, N.95, A.96, G.97, I.98, T.118, L.145, S.146, S.147, Y.160, K.164, P.190, G.191, I.193, S.195 Ligands: PG4.10 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.190 Hydrogen bonds: D:G.17, D:S.19, D:S.19, D:I.22, D:A.42, D:G.43, D:S.44, D:N.68, D:V.69, D:N.95, D:G.97, D:K.164, D:I.193, D:S.195, D:S.195 Water bridges: D:G.97, D:I.98 Salt bridges: D:R.20, D:R.20

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 7 residues within 4Å: Chain A: S.147, N.154, Q.157, Y.160, F.192, M.209 Ligands: NDP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.147, A:N.154, A:Q.157, A:Q.212 PG4.3: 4 residues within 4Å: Chain A: P.132, L.135, R.136, R.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.136, A:R.136 PG4.5: 9 residues within 4Å: Chain B: V.148, V.149, V.152, N.154, G.191, F.192, Q.212, M.250 Ligands: NDP.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.212 PG4.7: 7 residues within 4Å: Chain C: S.147, N.154, Q.157, Y.160, F.192, M.209 Ligands: NDP.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.147, C:N.154, C:Q.157, C:Y.160, C:Q.212 PG4.8: 4 residues within 4Å: Chain C: P.132, L.135, R.136, R.138 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.136, C:R.136 PG4.10: 9 residues within 4Å: Chain D: V.148, V.149, V.152, N.154, G.191, F.192, Q.212, M.250 Ligands: NDP.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dutta, D. et al., Crystal structure and fluorescence studies reveal the role of helical dimeric interface of staphylococcal fabg1 in positive cooperativity for NADPH. Proteins (2012)

Release Date

2012-01-25

Peptides

3-oxoacyl-(Acyl-carrier-protein) reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

3-oxoacyl-(Acyl-carrier-protein) reductase