SMTL ID : 6c5n.1

Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase with hydroxyoxamate inhibitor 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 27 residues within 4Å: Chain A: G.23, Y.24, G.25, S.26, Q.27, I.46, R.47, S.51, V.65, L.78, L.79, P.80, D.81, I.83, Q.84, V.87, A.105, H.106, P.128, G.130, P.131, G.132 Chain B: S.248, I.249, S.250 Ligands: EN4.4, 81B.5 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Q.27 Hydrogen bonds: A:Y.24, A:Y.24, A:S.26, A:Q.27, A:Q.27, A:R.47, A:R.47, A:S.51, A:S.51, A:S.51, A:L.79, A:D.81, A:Q.84, A:G.132, B:S.248 Water bridges: A:G.25, A:S.26, A:S.26, A:G.28, A:R.47, A:R.47, A:H.106, B:N.251, B:N.251, B:N.251 Salt bridges: A:R.47 pi-Cation interactions: A:R.47 NDP.8: 24 residues within 4Å: Chain A: S.248, I.249, S.250 Chain B: Y.24, G.25, S.26, Q.27, I.46, R.47, S.51, L.78, L.79, P.80, D.81, I.83, Q.84, A.105, H.106, P.128, G.130, P.131, G.132 Ligands: EN4.6, 81B.7 24 PLIP interactions: 4 interactions with chain A, 20 interactions with chain B Hydrogen bonds: A:S.248, A:I.249, B:Y.24, B:Y.24, B:S.26, B:Q.27, B:Q.27, B:R.47, B:S.51, B:S.51, B:L.79, B:D.81, B:Q.84, B:G.132 Water bridges: A:S.250, A:N.251, B:G.25, B:S.26, B:S.26, B:G.28, B:H.106 Hydrophobic interactions: B:Q.27 Salt bridges: B:R.47 pi-Cation interactions: B:R.47

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.189, E.193 Ligands: MG.3, EN4.4, 81B.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.189, A:E.193, H2O.3, H2O.8 MG.3: 4 residues within 4Å: Chain A: D.189 Ligands: MG.2, EN4.4, 81B.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.189, H2O.1, H2O.4, H2O.19, H2O.20 MG.9: 4 residues within 4Å: Chain B: D.189 Ligands: EN4.6, 81B.7, MG.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.189, H2O.2, H2O.17, H2O.17, H2O.20 MG.10: 5 residues within 4Å: Chain B: D.189, E.193 Ligands: EN4.6, 81B.7, MG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.189, B:E.193, H2O.19, H2O.24

2 x EN4: [cyclopentyl(hydroxy)amino](oxo)acetic acid(Non-covalent)

EN4.4: 13 residues within 4Å: Chain A: G.130, P.131, D.189, E.193, C.198 Chain B: E.229, I.249, S.250, A.253 Ligands: NDP.1, MG.2, MG.3, 81B.5 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.131, B:I.249 Hydrogen bonds: A:D.189, A:E.193, B:S.250, B:A.253 Water bridges: A:K.129, A:K.129, B:S.250 EN4.6: 14 residues within 4Å: Chain A: E.229, I.233, I.249, S.250, A.253 Chain B: G.130, P.131, D.189, E.193, C.198 Ligands: 81B.7, NDP.8, MG.9, MG.10 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.233, A:I.249, B:P.131 Hydrogen bonds: A:S.250, B:D.189 Water bridges: A:S.250

2 x 81B: (cyclopentylamino)(oxo)acetic acid(Non-covalent)

81B.5: 14 residues within 4Å: Chain A: G.130, P.131, D.189, E.193, C.198 Chain B: E.229, I.233, I.249, S.250, A.253 Ligands: NDP.1, MG.2, MG.3, EN4.4 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.233, B:I.249, A:P.131 Hydrogen bonds: B:E.229, B:S.250, A:E.193 Water bridges: B:S.250, A:K.129 81B.7: 14 residues within 4Å: Chain A: E.229, I.233, I.249, S.250, A.253 Chain B: G.130, P.131, D.189, E.193, C.198 Ligands: EN4.6, NDP.8, MG.9, MG.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.233, A:I.249, B:P.131 Hydrogen bonds: A:E.229, A:S.250 Water bridges: A:S.250

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.11: 6 residues within 4Å: Chain B: D.81, E.82, F.108, N.109, F.289, I.290 5 PLIP interactions: 5 interactions with chain B Water bridges: B:D.81, B:E.82, B:G.85, B:N.109, B:N.293

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 reductosiomerase (KARI) inhibitor. To Be Published

Release Date

2019-01-30

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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