SMTL ID : 5wj1.1

Crystal structure of Arabidopsis thaliana acetohydroxyacid synthase in complex with a triazolopyrimidine herbicide, penoxsulam

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.453, N.480, H.482, G.484 Ligands: TP9.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.453, A:H.482, H2O.6 MG.7: 5 residues within 4Å: Chain B: D.453, N.480, H.482, G.484 Ligands: TP9.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.453, B:H.482, H2O.32 MG.13: 5 residues within 4Å: Chain C: D.453, N.480, H.482, G.484 Ligands: TP9.18 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.453, C:H.482, H2O.57 MG.19: 5 residues within 4Å: Chain D: D.453, N.480, H.482, G.484 Ligands: TP9.24 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.453, D:H.482, H2O.83

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

FAD.2: 38 residues within 4Å: Chain A: L.99, R.161, G.222, G.223, G.224, T.246, L.247, M.248, M.263, L.264, G.265, M.266, H.267, G.268, G.286, V.287, R.288, D.290, R.292, V.293, I.309, D.310, I.311, D.312, E.315, G.328, D.329, V.330, V.400, Q.404, M.405, S.422, G.423, G.424, G.426, M.485 Chain D: F.121 Ligands: PXD.4 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.247, A:V.400, D:F.121 Hydrogen bonds: A:L.99, A:R.161, A:G.223, A:G.224, A:T.246, A:T.246, A:L.247, A:L.264, A:H.267, A:G.268, A:V.287, A:R.288, A:R.288, A:I.311, A:D.312, A:D.329, A:D.329, A:V.330, A:G.423 Water bridges: A:R.161, A:F.289, A:V.293, A:G.424 Salt bridges: A:R.288 pi-Stacking: D:F.121 FAD.8: 38 residues within 4Å: Chain B: L.99, R.161, G.222, G.223, G.224, T.246, L.247, M.248, M.263, L.264, G.265, M.266, H.267, G.268, G.286, V.287, R.288, D.290, R.292, V.293, I.309, D.310, I.311, D.312, E.315, G.328, D.329, V.330, V.400, Q.404, M.405, S.422, G.423, G.424, G.426, M.485 Chain C: F.121 Ligands: PXD.10 28 PLIP interactions: 26 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.247, B:V.400, C:F.121 Hydrogen bonds: B:L.99, B:R.161, B:G.223, B:G.224, B:T.246, B:T.246, B:L.247, B:L.264, B:H.267, B:G.268, B:V.287, B:R.288, B:R.288, B:I.311, B:D.312, B:D.329, B:D.329, B:V.330, B:G.423 Water bridges: B:R.161, B:F.289, B:V.293, B:G.424 Salt bridges: B:R.288 pi-Stacking: C:F.121 FAD.14: 38 residues within 4Å: Chain B: F.121 Chain C: L.99, R.161, G.222, G.223, G.224, T.246, L.247, M.248, M.263, L.264, G.265, M.266, H.267, G.268, G.286, V.287, R.288, D.290, R.292, V.293, I.309, D.310, I.311, D.312, E.315, G.328, D.329, V.330, V.400, Q.404, M.405, S.422, G.423, G.424, G.426, M.485 Ligands: PXD.16 26 PLIP interactions: 24 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.247, C:V.400, B:F.121 Hydrogen bonds: C:L.99, C:R.161, C:G.223, C:G.224, C:T.246, C:L.247, C:L.264, C:H.267, C:G.268, C:V.287, C:R.288, C:R.288, C:I.311, C:D.312, C:D.329, C:V.330, C:G.423 Water bridges: C:R.161, C:F.289, C:V.293, C:G.424 Salt bridges: C:R.288 pi-Stacking: B:F.121 FAD.20: 38 residues within 4Å: Chain A: F.121 Chain D: L.99, R.161, G.222, G.223, G.224, T.246, L.247, M.248, M.263, L.264, G.265, M.266, H.267, G.268, G.286, V.287, R.288, D.290, R.292, V.293, I.309, D.310, I.311, D.312, E.315, G.328, D.329, V.330, V.400, Q.404, M.405, S.422, G.423, G.424, G.426, M.485 Ligands: PXD.22 26 PLIP interactions: 24 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.247, D:V.400, A:F.121 Hydrogen bonds: D:L.99, D:R.161, D:G.223, D:G.224, D:T.246, D:L.247, D:L.264, D:H.267, D:G.268, D:V.287, D:R.288, D:R.288, D:I.311, D:D.312, D:D.329, D:V.330, D:G.423 Water bridges: D:R.161, D:F.289, D:V.293, D:G.424 Salt bridges: D:R.288 pi-Stacking: A:F.121

4 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: M.458, N.459, Q.461 Chain D: M.458, N.459, Q.461 Ligands: K.21 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:M.458, A:M.458 K.9: 7 residues within 4Å: Chain B: M.458, N.459, Q.461 Chain C: M.458, N.459, Q.461 Ligands: K.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:M.458, C:M.458 K.15: 7 residues within 4Å: Chain B: M.458, N.459, Q.461 Chain C: M.458, N.459, Q.461 Ligands: K.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:M.458, C:M.458 K.21: 7 residues within 4Å: Chain A: M.458, N.459, Q.461 Chain D: M.458, N.459, Q.461 Ligands: K.3 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:M.458, A:M.458

4 x PXD: 2-(2,2-difluoroethoxy)-N-(5,8-dimethoxy[1,2,4]triazolo[1,5-c]pyrimidin-2-yl)-6-(trifluoromethyl)benzenesulfonamide(Non-covalent)

PXD.4: 20 residues within 4Å: Chain A: M.266, D.291, R.292, M.485, V.486, W.489, S.568, G.569 Chain D: G.36, A.37, M.39, S.83, V.111, P.112, R.114, M.115, F.121, K.171 Ligands: FAD.2, F50.5 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:R.292, A:R.292, A:S.568, D:K.171, D:K.171 pi-Stacking: A:W.489, A:W.489 Hydrophobic interactions: D:V.111, D:F.121 Halogen bonds: D:S.83, D:K.171 PXD.10: 20 residues within 4Å: Chain B: M.266, D.291, R.292, M.485, V.486, W.489, S.568, G.569 Chain C: G.36, A.37, M.39, S.83, V.111, P.112, R.114, M.115, F.121, K.171 Ligands: FAD.8, F50.11 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.111, C:F.121 Hydrogen bonds: C:K.171, C:K.171, B:R.292, B:R.292, B:S.568 Halogen bonds: C:S.83, C:K.171 pi-Stacking: B:W.489, B:W.489 PXD.16: 20 residues within 4Å: Chain B: G.36, A.37, M.39, S.83, V.111, P.112, R.114, M.115, F.121, K.171 Chain C: M.266, D.291, R.292, M.485, V.486, W.489, S.568, G.569 Ligands: FAD.14, F50.17 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:V.111, B:F.121 Hydrogen bonds: B:K.171, B:K.171, C:R.292, C:R.292, C:S.568 Halogen bonds: B:S.83, B:K.171 pi-Stacking: C:W.489, C:W.489 PXD.22: 20 residues within 4Å: Chain A: G.36, A.37, M.39, S.83, V.111, P.112, R.114, M.115, F.121, K.171 Chain D: M.266, D.291, R.292, M.485, V.486, W.489, S.568, G.569 Ligands: FAD.20, F50.23 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:R.292, D:R.292, D:S.568, A:K.171, A:K.171 pi-Stacking: D:W.489, D:W.489 Hydrophobic interactions: A:V.111, A:F.121 Halogen bonds: A:S.83, A:K.171

4 x F50: ETHANEPEROXOIC ACID(Non-covalent)

F50.5: 7 residues within 4Å: Chain A: V.400, M.485 Chain D: G.35, G.36, Q.122 Ligands: PXD.4, TP9.6 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.36, D:Q.122 Water bridges: D:A.37, D:T.82 Hydrophobic interactions: A:M.485 F50.11: 7 residues within 4Å: Chain B: V.400, M.485 Chain C: G.35, G.36, Q.122 Ligands: PXD.10, TP9.12 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.36, C:Q.122 Water bridges: C:A.37, C:T.82 Hydrophobic interactions: B:M.485 F50.17: 7 residues within 4Å: Chain B: G.35, G.36, Q.122 Chain C: V.400, M.485 Ligands: PXD.16, TP9.18 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:M.485 Hydrogen bonds: B:G.36, B:Q.122 Water bridges: B:A.37, B:T.82 F50.23: 7 residues within 4Å: Chain A: G.35, G.36, Q.122 Chain D: V.400, M.485 Ligands: PXD.22, TP9.24 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.36, A:Q.122 Water bridges: A:A.37, A:T.82 Hydrophobic interactions: D:M.485

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: 26 residues within 4Å: Chain A: V.400, G.401, Q.402, H.403, G.426, M.428, G.452, D.453, G.454, S.455, M.458, N.480, H.482, L.483, G.484, M.485, V.486 Chain D: Y.33, P.34, G.35, E.59, P.85, N.89, Q.122 Ligands: MG.1, F50.5 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:M.428, A:L.483, A:L.483, A:V.486, D:Y.33, D:P.85 Hydrogen bonds: A:Q.402, A:H.403, A:G.426, A:M.428, A:D.453, A:G.454, A:S.455, A:N.480, A:G.484, A:M.485, D:Q.122 Water bridges: A:D.453, A:D.453, D:E.59 Salt bridges: A:H.403, A:H.403 TP9.12: 26 residues within 4Å: Chain B: V.400, G.401, Q.402, H.403, G.426, M.428, G.452, D.453, G.454, S.455, M.458, N.480, H.482, L.483, G.484, M.485, V.486 Chain C: Y.33, P.34, G.35, E.59, P.85, N.89, Q.122 Ligands: MG.7, F50.11 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:M.428, B:L.483, B:L.483, B:V.486, C:Y.33, C:P.85 Hydrogen bonds: B:Q.402, B:H.403, B:G.426, B:M.428, B:D.453, B:G.454, B:S.455, B:N.480, B:G.484, B:M.485, C:Q.122 Water bridges: B:D.453, B:D.453, C:E.59 Salt bridges: B:H.403, B:H.403 TP9.18: 26 residues within 4Å: Chain B: Y.33, P.34, G.35, E.59, P.85, N.89, Q.122 Chain C: V.400, G.401, Q.402, H.403, G.426, M.428, G.452, D.453, G.454, S.455, M.458, N.480, H.482, L.483, G.484, M.485, V.486 Ligands: MG.13, F50.17 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:M.428, C:L.483, C:L.483, C:V.486, B:Y.33, B:P.85 Hydrogen bonds: C:Q.402, C:H.403, C:G.426, C:M.428, C:D.453, C:G.454, C:S.455, C:N.480, C:G.484, C:M.485, B:Q.122 Salt bridges: C:H.403, C:H.403 TP9.24: 26 residues within 4Å: Chain A: Y.33, P.34, G.35, E.59, P.85, N.89, Q.122 Chain D: V.400, G.401, Q.402, H.403, G.426, M.428, G.452, D.453, G.454, S.455, M.458, N.480, H.482, L.483, G.484, M.485, V.486 Ligands: MG.19, F50.23 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:M.428, D:L.483, D:L.483, D:V.486, A:Y.33, A:P.85 Hydrogen bonds: D:Q.402, D:H.403, D:G.426, D:M.428, D:D.453, D:G.454, D:S.455, D:G.484, D:M.485, A:Q.122 Salt bridges: D:H.403, D:H.403

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lonhienne, T. et al., Structural insights into the mechanism of inhibition of AHAS by herbicides. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-02-14

Peptides

Acetolactate synthase, chloroplastic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Acetolactate synthase, chloroplastic

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