SMTL ID : 4d43.2 (1 other biounit)

Crystal structure of S. aureus FabI in complex with NADP and 2-(2- chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

3 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 4 residues within 4Å: Chain A: G.228, G.229, F.230, N.231 9 PLIP interactions: 5 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:G.229, A:F.230, A:N.231, E.1, E.1 Water bridges: A:N.231, E.1, E.1 Salt bridges: A:R.129 GLU.5: 5 residues within 4Å: Chain B: R.129, G.228, G.229, F.230, N.231 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:G.229, B:N.231, B:N.231, E.5, E.5 Water bridges: B:F.230, B:F.230 Salt bridges: B:R.129 GLU.9: 5 residues within 4Å: Chain C: R.129, G.228, G.229, F.230, N.231 8 PLIP interactions: 6 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:G.229, C:N.231, C:N.231, E.9, E.9 Water bridges: C:F.230, C:F.230 Salt bridges: C:R.129

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 8 residues within 4Å: Chain A: K.33, D.114, G.166, N.208, R.210, L.260, S.261, D.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.210, A:L.260 MRD.6: 8 residues within 4Å: Chain B: K.33, D.114, G.166, N.208, R.210, L.260, S.261, D.262 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.262 Hydrogen bonds: B:R.210, B:L.260, B:S.261 Water bridges: B:D.262 MRD.10: 7 residues within 4Å: Chain C: K.33, D.114, G.166, N.208, R.210, L.260, D.262 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.210, C:L.260, C:S.261 MRD.15: 9 residues within 4Å: Chain D: K.33, D.114, G.166, S.167, N.208, R.210, L.260, S.261, D.262 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:D.262 Hydrogen bonds: D:R.210, D:L.260

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.3: 28 residues within 4Å: Chain A: G.39, I.40, A.41, S.45, I.46, R.66, K.67, S.70, I.91, D.92, V.93, 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, L.222, S.223, F.230 Ligands: 9W7.4 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.46, A:Y.173, A:Y.173, A:A.216 Hydrogen bonds: A:G.39, A:I.46, A:R.66, A:K.67, A:S.70, A:S.70, 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:S.223 Water bridges: A:N.42, A:R.66, A:R.66, A:S.119, A:S.119, A:I.120, A:S.223 Salt bridges: A:R.66, A:K.67 NAP.7: 28 residues within 4Å: Chain B: 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: 9W7.8 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:I.46, B:Y.173, B:A.216 Hydrogen bonds: B:G.39, B:I.46, B:R.66, B:R.66, B:K.67, B:S.70, B:S.70, B:D.92, B:V.93, B:I.120, B:A.121, B:K.190, B:I.219, B:I.219, B:T.221, B:S.223 Water bridges: B:N.42, B:A.47, B:S.119, B:I.120 Salt bridges: B:R.66, B:K.67 NAP.11: 30 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, F.122, I.146, T.171, T.172, Y.173, K.190, A.216, G.217, P.218, I.219, T.221, L.222, S.223, F.230 Ligands: 9W7.12 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:I.46, C:Y.173, C:Y.173, C:A.216 Hydrogen bonds: C:G.39, C:I.46, C:R.66, C:K.67, C:S.70, C:S.70, C:D.92, C:V.93, C:I.120, C:K.190, C:I.219, C:I.219, C:S.223 Water bridges: C:N.42, C:A.47, C:R.66, C:S.119, C:I.120 Salt bridges: C:R.66, C:K.67 pi-Cation interactions: C:R.66 NAP.13: 27 residues within 4Å: Chain D: G.39, I.40, A.41, S.45, I.46, R.66, K.67, S.70, I.91, D.92, V.93, 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, L.222, S.223 Ligands: 9W7.14 30 PLIP interactions: 30 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:R.66, D:K.67, D:S.70, D:S.70, D:D.92, D:V.93, D:I.120, D:A.121, D:K.190, D:I.219, D:I.219, D:S.223 Water bridges: D:K.67, D:K.67, D:Q.94, D:S.119, D:S.119, D:T.171, D:L.222, D:S.223, D:S.223 Salt bridges: D:R.66, D:K.67

4 x 9W7: 2-(2-chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol(Non-covalent)

9W7.4: 13 residues within 4Å: Chain A: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, K.190, S.223, A.224, V.227, F.230 Ligands: NAP.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.128, A:Y.173, A:Y.173, A:Y.173, A:Y.183, A:V.227 Hydrogen bonds: A:A.123, A:Y.183 9W7.8: 12 residues within 4Å: Chain B: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, K.190, S.223, A.224, F.230 Ligands: NAP.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.128, B:Y.173, B:Y.173, B:Y.173, B:Y.183 Hydrogen bonds: B:A.123, B:Y.183 9W7.12: 14 residues within 4Å: Chain C: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, K.190, P.218, S.223, A.224, V.227, F.230 Ligands: NAP.11 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.128, C:Y.173, C:Y.173, C:Y.173, C:Y.183, C:P.218 Hydrogen bonds: C:A.123, C:Y.183, C:Y.183 9W7.14: 13 residues within 4Å: Chain D: A.121, F.122, A.123, L.128, Y.173, Y.183, M.186, K.190, S.223, A.224, V.227, F.230 Ligands: NAP.13 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.128, D:Y.173, D:Y.173, D:Y.183, D:V.227 Hydrogen bonds: D:A.123, D:Y.183 pi-Stacking: D:Y.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiebel, J. et al., An Ordered Water Channel in Staphylococcus Aureus Fabi: Unraveling the Mechanism of Substrate Recognition and Reduction. Biochemistry (2015)

Release Date

2015-03-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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