SMTL ID : 5w3k.1

Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex NADPH, Mg2+ and CPD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

2 x 9TY: cyclopropane-1,1-dicarboxylic acid(Non-covalent)

9TY.1: 10 residues within 4Å: Chain A: E.230, I.250, S.251, A.254 Chain B: P.132, D.190, E.194 Ligands: MG.8, MG.9, NDP.10 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.250 Hydrogen bonds: A:E.230, A:S.251 Water bridges: A:S.251, A:S.251, B:K.130, B:K.130, B:E.194, B:E.194 9TY.7: 10 residues within 4Å: Chain A: P.132, D.190, E.194 Chain B: E.230, I.250, S.251, A.254 Ligands: MG.2, MG.3, NDP.6 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.194, B:S.251 Water bridges: A:K.130, A:E.194, A:E.194, B:S.251, B:S.251 Hydrophobic interactions: B:I.250

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.130, D.190 Chain B: E.226, E.230 Ligands: MG.3, 9TY.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.190, H2O.3, H2O.15, H2O.16 MG.3: 4 residues within 4Å: Chain A: D.190, E.194 Ligands: MG.2, 9TY.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:E.194, H2O.2, H2O.7 MG.4: 5 residues within 4Å: Chain A: V.70, K.71, Q.72, A.73, N.101 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.70, A:K.71, A:A.73, H2O.2, H2O.6 MG.5: 2 residues within 4Å: Chain A: N.39, Y.41 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain A: E.226, E.230 Chain B: K.130, D.190 Ligands: 9TY.1, MG.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.190, H2O.1, H2O.3, H2O.16 MG.9: 4 residues within 4Å: Chain B: D.190, E.194 Ligands: 9TY.1, MG.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.190, B:E.194, H2O.15, H2O.21

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

NDP.6: 26 residues within 4Å: Chain A: 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 Chain B: S.249, I.250, S.251 Ligands: 9TY.7 28 PLIP interactions: 23 interactions with chain A, 5 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: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:G.26, A:R.48, A:P.49, A:D.82, A:H.107, B:S.249, B:I.250, B:S.251, B:N.252 Salt bridges: A:R.48 pi-Cation interactions: A:R.48 NDP.10: 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: 9TY.1 31 PLIP interactions: 7 interactions with chain A, 24 interactions with chain B Hydrogen bonds: A:S.249, B:Y.25, B:Y.25, 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:S.249, A:I.250, A:S.251, A:N.252, A:N.252, A:N.252, B:G.26, B:G.29, B:R.48, B:R.48, B:R.48, B:E.92, B:E.92, B:H.107 Salt bridges: B:R.48 pi-Cation interactions: B:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patel, K.M. et al., Crystal Structures of Staphylococcus aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues that Have Biocidal Activity. Chemistry (2017)

Release Date

2017-10-25

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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