SMTL ID : 6aqj.1

Crystal structures of Staphylococcus aureus ketol-acid reductoisomerase in complex with two transition state analogs that have biocidal activity.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.129, D.189 Chain B: E.229 Ligands: MG.2, 40E.3, HIO.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.189, H2O.1, H2O.3, H2O.4, H2O.16 MG.2: 5 residues within 4Å: Chain A: D.189, E.193 Ligands: MG.1, 40E.3, HIO.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.189, A:E.193, H2O.2, H2O.7 MG.11: 6 residues within 4Å: Chain A: E.229 Chain B: K.129, D.189 Ligands: 40E.9, HIO.10, MG.12 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.189, H2O.2, H2O.14, H2O.16, H2O.16 MG.12: 5 residues within 4Å: Chain B: D.189, E.193 Ligands: 40E.9, HIO.10, MG.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.189, B:E.193, H2O.17, H2O.21

2 x 40E: oxo(propan-2-ylamino)acetic acid(Non-covalent)

40E.3: 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: MG.1, MG.2, NDP.7, HIO.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.229, B:S.250 Water bridges: B:S.250 Hydrophobic interactions: A:P.131 40E.9: 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: HIO.10, MG.11, MG.12, NDP.16 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.229, A:S.250 Water bridges: A:S.250, B:K.129 Hydrophobic interactions: B:P.131

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: L.134, R.137, T.138, E.141 Chain B: K.231, D.235 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.137, A:E.141, B:D.235 Water bridges: A:E.141, A:S.143, A:S.143, B:K.231 GOL.5: 6 residues within 4Å: Chain A: Y.24, G.25, H.29, H.133 Chain B: Y.247 Ligands: GOL.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.24, B:Y.247 GOL.6: 6 residues within 4Å: Chain A: G.25, S.26, S.51 Chain B: Y.247 Ligands: GOL.5, NDP.7 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.51, B:Y.247 Water bridges: A:S.26, A:S.26 GOL.13: 6 residues within 4Å: Chain A: K.231, D.235 Chain B: L.134, R.137, T.138, E.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.137, B:E.141 Water bridges: B:S.143, B:S.143

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

NDP.7: 28 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: 40E.3, GOL.6, HIO.8 30 PLIP interactions: 23 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Y.24, A:Y.24, A:S.26, 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:G.28, A:R.47, A:R.47, A:R.47, A:H.106, B:S.248, B:I.249, B:S.250, B:N.251, B:N.251, B:N.251 Salt bridges: A:R.47 pi-Cation interactions: A:R.47 NDP.16: 26 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, 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 Ligands: 40E.9, HIO.10 30 PLIP interactions: 28 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.24, B:Y.24, B:S.26, B:Q.27, B:Q.27, B:R.47, B:R.47, B:S.51, B:S.51, B:S.51, B:L.79, B:D.81, B:Q.84, B:G.132, A:S.248 Water bridges: B:G.25, B:S.26, B:S.26, B:G.28, B:R.47, B:R.47, B:R.47, B:R.50, B:F.52, B:E.91, B:E.91, B:H.106, A:N.251 Salt bridges: B:R.47 pi-Cation interactions: B:R.47

2 x HIO: N-HYDROXY-N-ISOPROPYLOXAMIC ACID(Non-covalent)

HIO.8: 15 residues within 4Å: Chain A: G.130, P.131, D.189, E.193, L.197, C.198 Chain B: E.229, I.233, I.249, S.250, A.253 Ligands: MG.1, MG.2, 40E.3, NDP.7 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.131, A:L.197, B:I.249 Hydrogen bonds: B:S.250 Water bridges: B:S.250 HIO.10: 13 residues within 4Å: Chain A: E.229, I.233, I.249, S.250, A.253 Chain B: P.131, D.189, E.193, C.198 Ligands: 40E.9, MG.11, MG.12, NDP.16 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.131, A:I.249 Water bridges: B:K.129, A:S.250 Hydrogen bonds: A:S.250

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.14: 3 residues within 4Å: Chain B: H.29, K.54, H.133 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.133 Water bridges: A:Y.247, A:Y.247 EDO.15: 3 residues within 4Å: Chain A: A.215 Chain B: K.183, Q.281 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.215, B:K.183 Water bridges: B:K.183

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

2017-10-18

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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