SMTL ID : 7tzz.1

Crystal structure of arabidopsis thaliana acetohydroxyacid synthase P197T mutant in complex with bispyribac-sodium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-dimer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.453, N.480, H.482, G.484 Ligands: AUJ.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.453, A:H.482, H2O.5 MG.6: 7 residues within 4Å: Chain A: M.458, N.459, Q.461 Chain B: M.458, N.459, Q.461 Ligands: MG.17 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:M.458, B:M.458 MG.7: 1 residues within 4Å: Chain A: Q.206 No protein-ligand interaction detected (PLIP) MG.8: 7 residues within 4Å: Chain A: G.36, A.37, T.82, S.83, Q.122 Ligands: 6QL.14, AUJ.15 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.82, A:S.83 MG.11: 4 residues within 4Å: Chain A: F.370, T.372, Y.381, K.533 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain B: D.453, N.480, H.482, G.484 Ligands: AUJ.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.453, B:H.482, H2O.16 MG.17: 7 residues within 4Å: Chain A: M.458, N.459, Q.461 Chain B: M.458, N.459, Q.461 Ligands: MG.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:M.458, B:M.458 MG.18: 1 residues within 4Å: Chain B: Q.206 No protein-ligand interaction detected (PLIP) MG.19: 7 residues within 4Å: Chain B: G.36, A.37, T.82, S.83, Q.122 Ligands: 6QL.3, AUJ.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.82, B:S.83 MG.22: 4 residues within 4Å: Chain B: F.370, T.372, Y.381, K.533 No protein-ligand interaction detected (PLIP)

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

FAD.2: 36 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, Q.404, M.405, S.422, G.423, G.424 Chain B: F.121 Ligands: 6QL.3, AUJ.4 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B 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:D.100, A:R.161, A:D.290 Salt bridges: A:R.288 Hydrophobic interactions: B:F.121 FAD.13: 36 residues within 4Å: Chain A: F.121 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, Q.404, M.405, S.422, G.423, G.424 Ligands: 6QL.14, AUJ.15 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.99, B:R.161, B:G.223, B:G.224, 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:V.330, B:G.423 Water bridges: B:R.161, B:D.290 Salt bridges: B:R.288 Hydrophobic interactions: A:F.121

2 x 6QL: 2,6-bis[(4,6-dimethoxypyrimidin-2-yl)oxy]benzoic acid(Non-covalent)

6QL.3: 19 residues within 4Å: Chain A: M.266, D.291, R.292, M.485, W.489, S.568, G.569 Chain B: G.36, A.37, M.39, V.111, T.112, M.115, F.121, K.171, Q.175 Ligands: FAD.2, AUJ.4, MG.19 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.292, A:R.292, A:S.568 Salt bridges: A:R.292, B:K.171 pi-Stacking: A:W.489 Hydrophobic interactions: B:V.111, B:T.112, B:F.121 Water bridges: B:K.171, B:K.171 6QL.14: 19 residues within 4Å: Chain A: G.36, A.37, M.39, V.111, T.112, M.115, F.121, K.171, Q.175 Chain B: M.266, D.291, R.292, M.485, W.489, S.568, G.569 Ligands: MG.8, FAD.13, AUJ.15 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.292, B:R.292, B:S.568 Salt bridges: B:R.292, A:K.171 pi-Stacking: B:W.489 Hydrophobic interactions: A:V.111, A:T.112, A:F.121 Water bridges: A:K.171, A:K.171

2 x AUJ: 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(1~{S})-1-(dioxidanyl)-1-oxidanyl-ethyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate(Non-covalent)

AUJ.4: 31 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 B: Y.33, P.34, G.35, G.36, E.59, T.82, P.85, N.89, F.121, Q.122 Ligands: MG.1, FAD.2, 6QL.3, MG.19 23 PLIP interactions: 5 interactions with chain B, 18 interactions with chain A Hydrophobic interactions: B:Y.33, B:T.82, B:P.85, A:M.428, A:L.483, A:V.486 Hydrogen bonds: B:G.36, B:Q.122, A:Q.402, A:Q.402, A:H.403, A:G.426, A:M.428, A:G.452, A:G.454, A:S.455, A:N.480, A:G.484, A:M.485 Water bridges: A:D.453, A:D.453 Salt bridges: A:H.403, A:H.403 AUJ.15: 31 residues within 4Å: Chain A: Y.33, P.34, G.35, G.36, E.59, T.82, P.85, N.89, F.121, Q.122 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 Ligands: MG.8, MG.12, FAD.13, 6QL.14 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:M.428, B:L.483, B:V.486, A:Y.33, A:T.82, A:P.85 Hydrogen bonds: B:Q.402, B:Q.402, B:H.403, B:G.426, B:M.428, B:G.452, B:G.454, B:S.455, B:N.480, B:G.484, B:M.485, A:G.36, A:Q.122 Water bridges: B:D.453, B:D.453 Salt bridges: B:H.403, B:H.403

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: E.28, T.29, Y.69, K.75, V.440, A.441 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.29, A:Y.69 Salt bridges: A:K.75 PO4.16: 6 residues within 4Å: Chain B: E.28, T.29, Y.69, K.75, V.440, A.441 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.29 Salt bridges: B:K.75

2 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.9: 8 residues within 4Å: Chain A: K.135, H.136, R.187, L.188, P.189, G.190, Y.191, R.194 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.191 Hydrogen bonds: A:G.190, A:Y.191, A:R.194 NHE.20: 8 residues within 4Å: Chain B: K.135, H.136, R.187, L.188, P.189, G.190, Y.191, R.194 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.191 Hydrogen bonds: B:G.190, B:Y.191, B:R.194

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain A: G.353, N.357, N.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.360 SO4.21: 3 residues within 4Å: Chain B: G.353, N.357, N.360 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.360

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lonhienne, T. et al., Structural basis of resistance to herbicides that target acetohydroxyacid synthase. Nat Commun (2022)

Release Date

2022-06-01

Peptides

Acetolactate synthase, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Acetolactate synthase, chloroplastic

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