SMTL ID : 6c55.1

Crystal structure of Staphylococcus aureus Ketol-acid Reductosimerrase with hydroxyoxamate inhibitor 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.190, E.194 Ligands: MG.2, EKD.4, EKA.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:E.194, H2O.2, H2O.4 MG.2: 7 residues within 4Å: Chain A: K.130, D.190 Chain B: E.226, E.230 Ligands: MG.1, EKD.4, EKA.7 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.190, H2O.1, H2O.1, H2O.1, H2O.5 MG.5: 6 residues within 4Å: Chain A: E.226, E.230 Chain B: K.130, D.190 Ligands: EKD.6, MG.8 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.230, B:D.190, H2O.1, H2O.5, H2O.8 MG.8: 4 residues within 4Å: Chain B: D.190, E.194 Ligands: MG.5, EKD.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.190, B:E.194, H2O.4, H2O.8

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

NAP.3: 24 residues within 4Å: Chain A: Y.25, G.26, S.27, Q.28, I.47, R.48, S.52, L.79, L.80, P.81, D.82, I.84, Q.85, A.106, H.107, P.129, G.131, P.132, G.133 Chain B: S.249, I.250, S.251 Ligands: EKD.4, EKA.7 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.28 Hydrogen bonds: A:Y.25, A:Y.25, A:S.27, A:S.27, A:Q.28, A:Q.28, A:R.48, A:S.52, A:S.52, A:L.80, A:D.82, A:Q.85, A:G.133, B:S.249 Water bridges: A:G.26, A:S.27, A:S.27, A:G.29, A:R.51, A:R.51, A:H.107, B:S.251 Salt bridges: A:R.48 pi-Cation interactions: A:R.48 NAP.9: 26 residues within 4Å: Chain A: S.249, I.250, S.251 Chain B: G.24, Y.25, G.26, S.27, Q.28, I.47, R.48, S.52, V.66, L.79, L.80, P.81, D.82, I.84, Q.85, V.88, A.106, H.107, P.129, G.131, P.132, G.133 Ligands: EKD.6 28 PLIP interactions: 5 interactions with chain A, 23 interactions with chain B Hydrogen bonds: A:S.249, A:S.251, B:Y.25, B:Y.25, B:S.27, B:S.27, B:S.27, B:Q.28, B:Q.28, B:R.48, B:R.48, B:S.52, B:S.52, B:L.80, B:D.82, B:Q.85, B:G.133 Water bridges: A:N.252, A:N.252, A:N.252, B:G.26, B:G.29, B:P.49, B:F.53, B:H.107 Hydrophobic interactions: B:Q.28 Salt bridges: B:R.48 pi-Cation interactions: B:R.48

2 x EKD: (cyclohexylamino)(oxo)acetic acid(Non-covalent)

EKD.4: 14 residues within 4Å: Chain A: P.132, D.190, E.194, L.198, C.199 Chain B: E.230, I.234, I.250, S.251, A.254 Ligands: MG.1, MG.2, NAP.3, EKA.7 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.230, B:I.234, B:I.250, A:L.198 Hydrogen bonds: B:E.230, B:S.251, A:E.194 Water bridges: B:S.251, A:K.130 EKD.6: 10 residues within 4Å: Chain A: I.250, S.251, A.254 Chain B: G.131, P.132, D.190, E.194 Ligands: MG.5, MG.8, NAP.9 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.132 Water bridges: B:K.130, B:K.130, B:E.194, A:E.226, A:S.251, A:S.251 Hydrogen bonds: A:S.251

1 x EKA: [cyclohexyl(hydroxy)amino](oxo)acetic acid(Non-covalent)

EKA.7: 14 residues within 4Å: Chain A: P.132, D.190, E.194, L.198, C.199 Chain B: E.230, I.234, I.250, S.251, A.254 Ligands: MG.1, MG.2, NAP.3, EKD.4 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:E.230, B:I.234, B:I.250, A:P.132, A:L.198, A:L.198 Hydrogen bonds: B:S.251 Water bridges: B:E.226, B:S.251, A:P.129, A:K.130, A:K.130, A:D.190, A:E.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kandale, A. et al., Design, synthesis, in vitro activity and crystallisation of novel N-isopropyl-N-hydroxyoxamate derivatives as ketol-acid reductoisomerase (KARI) inhibitors. To Be Published

Release Date

2019-01-16

Peptides

Ketol-acid reductoisomerase (NADP(+)): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ketol-acid reductoisomerase (NADP(+))

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