SMTL ID : 6dep.1

Crystal structure of Candida albicans acetohydroxyacid synthase in complex with the herbicide sulfometuron methyl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 38 residues within 4Å: Chain A: M.174, D.175, R.236, G.302, A.303, G.304, N.307, T.329, L.330, Q.331, M.346, L.347, G.348, M.349, H.350, G.351, G.369, A.370, R.371, D.373, R.375, V.376, F.401, E.402, I.403, S.404, N.407, G.420, D.421, V.422, V.492, Q.496, M.497, S.514, G.515, G.516 Chain D: F.196 Ligands: 1SM.4 30 PLIP interactions: 28 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:V.492, D:F.196, D:F.196 Hydrogen bonds: A:M.174, A:R.236, A:A.303, A:G.304, A:N.307, A:T.329, A:T.329, A:L.330, A:Q.331, A:L.347, A:H.350, A:G.351, A:R.371, A:I.403, A:N.407, A:D.421, A:V.422, A:G.515 Water bridges: A:D.175, A:R.236, A:R.236, A:G.369, A:R.371, A:F.372, A:T.423 Salt bridges: A:R.236, A:R.371 FAD.7: 38 residues within 4Å: Chain B: M.174, D.175, R.236, G.302, A.303, G.304, N.307, T.329, L.330, Q.331, M.346, L.347, G.348, M.349, H.350, G.351, G.369, A.370, R.371, D.373, R.375, V.376, F.401, E.402, I.403, S.404, N.407, G.420, D.421, V.422, V.492, Q.496, M.497, S.514, G.515, G.516 Chain C: F.196 Ligands: 1SM.10 30 PLIP interactions: 28 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.492, C:F.196, C:F.196 Hydrogen bonds: B:M.174, B:R.236, B:A.303, B:G.304, B:N.307, B:T.329, B:T.329, B:L.330, B:Q.331, B:L.347, B:H.350, B:G.351, B:R.371, B:I.403, B:N.407, B:D.421, B:V.422, B:G.515 Water bridges: B:D.175, B:R.236, B:R.236, B:G.369, B:R.371, B:F.372, B:T.423 Salt bridges: B:R.236, B:R.371 FAD.13: 38 residues within 4Å: Chain B: F.196 Chain C: M.174, D.175, R.236, G.302, A.303, G.304, N.307, T.329, L.330, Q.331, M.346, L.347, G.348, M.349, H.350, G.351, G.369, A.370, R.371, D.373, R.375, V.376, F.401, E.402, I.403, S.404, N.407, G.420, D.421, V.422, V.492, Q.496, M.497, S.514, G.515, G.516 Ligands: 1SM.16 30 PLIP interactions: 28 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.492, B:F.196, B:F.196 Hydrogen bonds: C:M.174, C:R.236, C:A.303, C:G.304, C:N.307, C:T.329, C:L.330, C:Q.331, C:L.347, C:H.350, C:G.351, C:R.371, C:I.403, C:N.407, C:D.421, C:D.421, C:V.422, C:G.515 Water bridges: C:R.236, C:R.236, C:G.369, C:R.371, C:R.371, C:F.372, C:T.423 Salt bridges: C:R.236, C:R.371 FAD.19: 38 residues within 4Å: Chain A: F.196 Chain D: M.174, D.175, R.236, G.302, A.303, G.304, N.307, T.329, L.330, Q.331, M.346, L.347, G.348, M.349, H.350, G.351, G.369, A.370, R.371, D.373, R.375, V.376, F.401, E.402, I.403, S.404, N.407, G.420, D.421, V.422, V.492, Q.496, M.497, S.514, G.515, G.516 Ligands: 1SM.22 30 PLIP interactions: 28 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:V.492, A:F.196, A:F.196 Hydrogen bonds: D:M.174, D:R.236, D:A.303, D:G.304, D:N.307, D:T.329, D:L.330, D:Q.331, D:L.347, D:H.350, D:G.351, D:R.371, D:I.403, D:N.407, D:D.421, D:D.421, D:V.422, D:G.515 Water bridges: D:R.236, D:R.236, D:G.369, D:R.371, D:R.371, D:F.372, D:T.423 Salt bridges: D:R.236, D:R.371

4 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: Q.338, D.345, Q.501, F.503 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.345, A:Q.501, A:F.503, H2O.2, H2O.17 K.8: 4 residues within 4Å: Chain B: Q.338, D.345, Q.501, F.503 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.345, B:Q.501, B:F.503, H2O.26, H2O.41 K.14: 4 residues within 4Å: Chain C: Q.338, D.345, Q.501, F.503 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.345, C:Q.501, C:F.503, H2O.51, H2O.66 K.20: 4 residues within 4Å: Chain D: Q.338, D.345, Q.501, F.503 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.345, D:Q.501, D:F.503, H2O.75, H2O.90

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.545, N.572, E.574, G.576 Ligands: TZD.5, TP9.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.545, A:E.574, H2O.4 MG.9: 6 residues within 4Å: Chain B: D.545, N.572, E.574, G.576 Ligands: TZD.11, TP9.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.545, B:E.574, H2O.28 MG.15: 6 residues within 4Å: Chain C: D.545, N.572, E.574, G.576 Ligands: TZD.17, TP9.18 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.545, C:E.574, H2O.52 MG.21: 6 residues within 4Å: Chain D: D.545, N.572, E.574, G.576 Ligands: TZD.23, TP9.24 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.545, D:E.574, H2O.77

4 x 1SM: METHYL 2-[({[(4,6-DIMETHYLPYRIMIDIN-2-YL)AMINO]CARBONYL}AMINO)SULFONYL]BENZOATE(Non-covalent)

1SM.4: 16 residues within 4Å: Chain A: M.349, D.374, R.375, M.577, V.578, W.581, A.652 Chain D: G.111, A.112, V.186, P.187, A.195, F.196, Q.197, K.246 Ligands: FAD.1 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:V.186, D:A.195, D:F.196, A:W.581 Hydrogen bonds: D:K.246, D:K.246, A:R.375, A:R.375 Water bridges: D:G.111 pi-Stacking: A:W.581, A:W.581 pi-Cation interactions: A:R.375 1SM.10: 16 residues within 4Å: Chain B: M.349, D.374, R.375, M.577, V.578, W.581, A.652 Chain C: G.111, A.112, V.186, P.187, A.195, F.196, Q.197, K.246 Ligands: FAD.7 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:V.186, C:A.195, C:F.196, B:W.581 Hydrogen bonds: C:K.246, C:K.246, B:R.375, B:R.375 Water bridges: C:G.111 pi-Stacking: B:W.581, B:W.581 pi-Cation interactions: B:R.375 1SM.16: 16 residues within 4Å: Chain B: G.111, A.112, V.186, P.187, A.195, F.196, Q.197, K.246 Chain C: M.349, D.374, R.375, M.577, V.578, W.581, A.652 Ligands: FAD.13 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:V.186, B:A.195, B:F.196, C:W.581 Hydrogen bonds: B:K.246, B:K.246, C:R.375, C:R.375 Water bridges: B:G.111 pi-Stacking: C:W.581, C:W.581 pi-Cation interactions: C:R.375 1SM.22: 16 residues within 4Å: Chain A: G.111, A.112, V.186, P.187, A.195, F.196, Q.197, K.246 Chain D: M.349, D.374, R.375, M.577, V.578, W.581, A.652 Ligands: FAD.19 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:V.186, A:A.195, A:F.196, D:W.581 Hydrogen bonds: A:K.246, A:K.246, D:R.375, D:R.375 Water bridges: A:G.111 pi-Stacking: D:W.581, D:W.581 pi-Cation interactions: D:R.375

4 x TZD: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TZD.5: 27 residues within 4Å: Chain A: V.492, G.493, Q.494, H.495, G.518, M.520, G.544, D.545, A.546, S.547, M.550, N.572, E.574, Q.575, G.576, M.577, V.578 Chain D: Y.108, A.109, G.110, E.134, T.157, P.160, N.164, Q.197 Ligands: MG.3, TP9.6 17 PLIP interactions: 4 interactions with chain D, 13 interactions with chain A Hydrophobic interactions: D:Y.108, D:P.160, A:Q.575 Hydrogen bonds: D:Q.197, A:Q.494, A:H.495, A:G.518, A:M.520, A:D.545, A:A.546, A:S.547, A:N.572, A:G.576, A:M.577 Water bridges: D:E.134 Salt bridges: A:H.495, A:H.495 TZD.11: 27 residues within 4Å: Chain B: V.492, G.493, Q.494, H.495, G.518, M.520, G.544, D.545, A.546, S.547, M.550, N.572, E.574, Q.575, G.576, M.577, V.578 Chain C: Y.108, A.109, G.110, E.134, T.157, P.160, N.164, Q.197 Ligands: MG.9, TP9.12 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Q.575, C:Y.108, C:P.160 Hydrogen bonds: B:Q.494, B:H.495, B:G.518, B:M.520, B:D.545, B:A.546, B:S.547, B:N.572, B:G.576, B:M.577, C:Q.197 Salt bridges: B:H.495, B:H.495 Water bridges: C:E.134 TZD.17: 27 residues within 4Å: Chain B: Y.108, A.109, G.110, E.134, T.157, P.160, N.164, Q.197 Chain C: V.492, G.493, Q.494, H.495, G.518, M.520, G.544, D.545, A.546, S.547, M.550, N.572, E.574, Q.575, G.576, M.577, V.578 Ligands: MG.15, TP9.18 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Q.575, B:Y.108, B:P.160 Hydrogen bonds: C:Q.494, C:H.495, C:G.518, C:M.520, C:D.545, C:A.546, C:S.547, C:N.572, C:E.574, C:G.576, C:M.577, B:Q.197 Salt bridges: C:H.495, C:H.495 TZD.23: 27 residues within 4Å: Chain A: Y.108, A.109, G.110, E.134, T.157, P.160, N.164, Q.197 Chain D: V.492, G.493, Q.494, H.495, G.518, M.520, G.544, D.545, A.546, S.547, M.550, N.572, E.574, Q.575, G.576, M.577, V.578 Ligands: MG.21, TP9.24 16 PLIP interactions: 3 interactions with chain A, 13 interactions with chain D Hydrophobic interactions: A:Y.108, A:P.160, D:Q.575 Hydrogen bonds: A:Q.197, D:Q.494, D:H.495, D:G.518, D:M.520, D:D.545, D:A.546, D:S.547, D:N.572, D:G.576, D:M.577 Salt bridges: D:H.495, D:H.495

4 x TP9: (3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TP9.6: 27 residues within 4Å: Chain A: V.492, G.493, Q.494, H.495, G.518, M.520, G.544, D.545, A.546, S.547, M.550, N.572, E.574, Q.575, G.576, M.577, V.578 Chain D: Y.108, A.109, G.110, E.134, T.157, P.160, N.164, Q.197 Ligands: MG.3, TZD.5 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:M.520, A:Q.575, D:Y.108, D:P.160 Hydrogen bonds: A:Q.494, A:H.495, A:G.518, A:M.520, A:D.545, A:A.546, A:S.547, A:N.572, A:G.576, A:M.577, D:Q.197 Salt bridges: A:H.495, A:H.495 Water bridges: D:G.111, D:Q.197, D:Q.197 TP9.12: 27 residues within 4Å: Chain B: V.492, G.493, Q.494, H.495, G.518, M.520, G.544, D.545, A.546, S.547, M.550, N.572, E.574, Q.575, G.576, M.577, V.578 Chain C: Y.108, A.109, G.110, E.134, T.157, P.160, N.164, Q.197 Ligands: MG.9, TZD.11 20 PLIP interactions: 6 interactions with chain C, 14 interactions with chain B Hydrophobic interactions: C:Y.108, C:P.160, B:M.520, B:Q.575 Hydrogen bonds: C:Q.197, B:Q.494, B:H.495, B:G.518, B:M.520, B:D.545, B:A.546, B:S.547, B:N.572, B:G.576, B:M.577 Water bridges: C:G.111, C:Q.197, C:Q.197 Salt bridges: B:H.495, B:H.495 TP9.18: 27 residues within 4Å: Chain B: Y.108, A.109, G.110, E.134, T.157, P.160, N.164, Q.197 Chain C: V.492, G.493, Q.494, H.495, G.518, M.520, G.544, D.545, A.546, S.547, M.550, N.572, E.574, Q.575, G.576, M.577, V.578 Ligands: MG.15, TZD.17 20 PLIP interactions: 14 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:M.520, C:Q.575, B:Y.108, B:P.160 Hydrogen bonds: C:Q.494, C:H.495, C:G.518, C:M.520, C:D.545, C:A.546, C:S.547, C:N.572, C:G.576, C:M.577, B:Q.197 Salt bridges: C:H.495, C:H.495 Water bridges: B:G.111, B:Q.197, B:Q.197 TP9.24: 27 residues within 4Å: Chain A: Y.108, A.109, G.110, E.134, T.157, P.160, N.164, Q.197 Chain D: V.492, G.493, Q.494, H.495, G.518, M.520, G.544, D.545, A.546, S.547, M.550, N.572, E.574, Q.575, G.576, M.577, V.578 Ligands: MG.21, TZD.23 20 PLIP interactions: 6 interactions with chain A, 14 interactions with chain D Hydrophobic interactions: A:Y.108, A:P.160, D:M.520, D:Q.575 Hydrogen bonds: A:Q.197, D:Q.494, D:H.495, D:G.518, D:M.520, D:D.545, D:A.546, D:S.547, D:N.572, D:G.576, D:M.577 Water bridges: A:G.111, A:Q.197, A:Q.197 Salt bridges: D:H.495, D:H.495

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia, M.D. et al., Commercial AHAS-inhibiting herbicides are promising drug leads for the treatment of human fungal pathogenic infections. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-26

Peptides

Acetolactate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Acetolactate synthase

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