SMTL ID : 8et4.1

Crystal structure of wild-type arabidopsis thaliana acetohydroxyacid synthase in complex with amidosulfuron

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.453, N.480, H.482, G.484 Ligands: AUJ.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.453, A:H.482, H2O.1 MG.7: 7 residues within 4Å: Chain A: M.458, N.459, Q.461 Chain D: M.458, N.459, Q.461 Ligands: MG.37 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:M.458, A:M.458 MG.8: 4 residues within 4Å: Chain A: F.370, T.372, Y.381, K.533 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain B: D.453, N.480, H.482, G.484 Ligands: AUJ.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.453, B:H.482, H2O.1 MG.17: 7 residues within 4Å: Chain B: M.458, N.459, Q.461 Chain C: M.458, N.459, Q.461 Ligands: MG.27 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:M.458, B:M.458 MG.18: 4 residues within 4Å: Chain B: F.370, T.372, Y.381, K.533 No protein-ligand interaction detected (PLIP) MG.21: 5 residues within 4Å: Chain C: D.453, N.480, H.482, G.484 Ligands: AUJ.26 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.453, C:H.482, H2O.1 MG.27: 7 residues within 4Å: Chain B: M.458, N.459, Q.461 Chain C: M.458, N.459, Q.461 Ligands: MG.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:M.458, B:M.458 MG.28: 4 residues within 4Å: Chain C: F.370, T.372, Y.381, K.533 No protein-ligand interaction detected (PLIP) MG.31: 5 residues within 4Å: Chain D: D.453, N.480, H.482, G.484 Ligands: AUJ.36 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.453, D:H.482, H2O.1 MG.37: 7 residues within 4Å: Chain A: M.458, N.459, Q.461 Chain D: M.458, N.459, Q.461 Ligands: MG.7 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:M.458, A:M.458 MG.38: 4 residues within 4Å: Chain D: F.370, T.372, Y.381, K.533 No protein-ligand interaction detected (PLIP)

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

FAD.2: 37 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, 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 Chain D: F.121 Ligands: WRQ.3, AUJ.6 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:V.400, D:F.121 Hydrogen bonds: A:L.99, A:S.101, A:R.161, A:G.223, A:G.224, A:T.246, A:L.247, A:L.264, A:H.267, A:G.268, A:R.288, A:R.288, A:D.290, A:I.311, A:D.312, A:D.329, A:D.329, A:V.330, A:G.423 Salt bridges: A:R.288 pi-Stacking: D:F.121 FAD.12: 37 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, 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 Chain C: F.121 Ligands: WRQ.13, AUJ.16 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.400, C:F.121 Hydrogen bonds: B:L.99, B:S.101, 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:R.288, B:R.288, B:D.290, B:I.311, B:D.312, B:D.329, B:D.329, B:V.330, B:G.423 Salt bridges: B:R.288 pi-Stacking: C:F.121 FAD.22: 37 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, 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 Ligands: WRQ.23, AUJ.26 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.400, B:F.121 Hydrogen bonds: C:L.99, C:S.101, C:R.161, C:G.223, C:G.224, C:T.246, C:T.246, C:L.247, C:L.264, C:H.267, C:G.268, C:R.288, C:R.288, C:I.311, C:D.312, C:D.329, C:V.330, C:G.423 Salt bridges: C:R.288 pi-Stacking: B:F.121 FAD.32: 37 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, 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 Ligands: WRQ.33, AUJ.36 22 PLIP interactions: 20 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:V.400, A:F.121 Hydrogen bonds: D:L.99, D:S.101, D:R.161, D:G.223, D:G.224, D:T.246, D:T.246, D:L.247, D:L.264, D:H.267, D:G.268, D:R.288, D:R.288, D:I.311, D:D.312, D:D.329, D:V.330, D:G.423 Salt bridges: D:R.288 pi-Stacking: A:F.121

4 x WRQ: N-{[(4,6-dimethoxypyrimidin-2-yl)carbamoyl]sulfamoyl}-N-methylmethanesulfonamide(Non-covalent)

WRQ.3: 17 residues within 4Å: Chain A: M.266, H.267, R.292, M.485, V.486, W.489, S.568 Chain D: G.36, A.37, M.39, Q.110, V.111, P.112, F.121, K.171 Ligands: FAD.2, AUJ.6 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:R.292, A:R.292, A:S.568, D:K.171, D:K.171, D:K.171 pi-Stacking: A:W.489, A:W.489 WRQ.13: 17 residues within 4Å: Chain B: M.266, H.267, R.292, M.485, V.486, W.489, S.568 Chain C: G.36, A.37, M.39, Q.110, V.111, P.112, F.121, K.171 Ligands: FAD.12, AUJ.16 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.292, B:R.292, B:S.568, C:K.171, C:K.171, C:K.171 pi-Stacking: B:W.489, B:W.489 WRQ.23: 17 residues within 4Å: Chain B: G.36, A.37, M.39, Q.110, V.111, P.112, F.121, K.171 Chain C: M.266, H.267, R.292, M.485, V.486, W.489, S.568 Ligands: FAD.22, AUJ.26 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:K.171, B:K.171, B:K.171, C:R.292, C:R.292, C:S.568 pi-Stacking: C:W.489, C:W.489 WRQ.33: 17 residues within 4Å: Chain A: G.36, A.37, M.39, Q.110, V.111, P.112, F.121, K.171 Chain D: M.266, H.267, R.292, M.485, V.486, W.489, S.568 Ligands: FAD.32, AUJ.36 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:K.171, A:K.171, A:K.171, D:R.292, D:R.292, D:S.568 pi-Stacking: D:W.489, D:W.489

4 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.4: 6 residues within 4Å: Chain A: E.28, T.29, Y.69, K.75, V.440, A.441 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.28, A:T.29, A:Y.69, A:A.441 Salt bridges: A:K.75, A:K.75 TLA.14: 6 residues within 4Å: Chain B: E.28, T.29, Y.69, K.75, V.440, A.441 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.28, B:T.29, B:Y.69, B:A.441 Salt bridges: B:K.75, B:K.75 TLA.24: 6 residues within 4Å: Chain C: E.28, T.29, Y.69, K.75, V.440, A.441 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.28, C:A.441 Salt bridges: C:K.75, C:K.75 TLA.34: 6 residues within 4Å: Chain D: E.28, T.29, Y.69, K.75, V.440, A.441 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.28, D:A.441 Salt bridges: D:K.75, D:K.75

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

NHE.5: 9 residues within 4Å: Chain A: K.135, H.136, L.156, R.187, L.188, P.189, G.190, Y.191, R.194 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.156 Hydrogen bonds: A:G.190, A:Y.191 Salt bridges: A:R.194 NHE.15: 9 residues within 4Å: Chain B: K.135, H.136, L.156, R.187, L.188, P.189, G.190, Y.191, R.194 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.156 Hydrogen bonds: B:G.190, B:Y.191 Salt bridges: B:R.194 NHE.25: 9 residues within 4Å: Chain C: K.135, H.136, L.156, R.187, L.188, P.189, G.190, Y.191, R.194 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.156 Hydrogen bonds: C:G.190, C:Y.191 Salt bridges: C:R.194 NHE.35: 9 residues within 4Å: Chain D: K.135, H.136, L.156, R.187, L.188, P.189, G.190, Y.191, R.194 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.156 Hydrogen bonds: D:G.190, D:Y.191 Salt bridges: D:R.194

4 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.6: 29 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, G.36, E.59, T.82, P.85, N.89, Q.122 Ligands: MG.1, FAD.2, WRQ.3 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:M.428, A:L.483, A:L.483, A:V.486, D:Y.33 Hydrogen bonds: A:Q.402, A:H.403, A:G.426, A:G.426, A:M.428, A:G.454, A:S.455, A:N.480, A:G.484, A:M.485, D:G.36, D:Q.122 Water bridges: A:D.453, A:D.453 Salt bridges: A:H.403, A:H.403 AUJ.16: 29 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, G.36, E.59, T.82, P.85, N.89, Q.122 Ligands: MG.11, FAD.12, WRQ.13 21 PLIP interactions: 3 interactions with chain C, 18 interactions with chain B Hydrophobic interactions: C:Y.33, B:M.428, B:L.483, B:L.483, B:V.486 Hydrogen bonds: C:G.36, C:Q.122, B:Q.402, B:H.403, B:G.426, B:G.426, B:M.428, B:G.454, B:S.455, B:N.480, B:G.484, B:M.485 Water bridges: B:D.453, B:D.453 Salt bridges: B:H.403, B:H.403 AUJ.26: 29 residues within 4Å: Chain B: Y.33, P.34, G.35, G.36, E.59, T.82, 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.21, FAD.22, WRQ.23 21 PLIP interactions: 3 interactions with chain B, 18 interactions with chain C Hydrophobic interactions: B:Y.33, C:M.428, C:L.483, C:L.483, C:V.486 Hydrogen bonds: B:G.36, B:Q.122, C:Q.402, C:H.403, C:G.426, C:G.426, C:M.428, C:G.454, C:S.455, C:N.480, C:G.484, C:M.485 Water bridges: C:D.453, C:D.453 Salt bridges: C:H.403, C:H.403 AUJ.36: 29 residues within 4Å: Chain A: Y.33, P.34, G.35, G.36, E.59, T.82, 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.31, FAD.32, WRQ.33 21 PLIP interactions: 18 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 Hydrogen bonds: D:Q.402, D:H.403, D:G.426, D:G.426, D:M.428, D:G.454, D:S.455, D:N.480, D:G.484, D:M.485, A:G.36, A:Q.122 Water bridges: D:D.453, D:D.453 Salt bridges: D:H.403, D:H.403

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

SO4.9: 6 residues within 4Å: Chain A: R.71, L.226, M.248, W.419, L.420, S.421 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.421 Salt bridges: A:R.71 SO4.10: 4 residues within 4Å: Chain A: W.489, Y.494 Chain D: K.171, Q.175 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.175 Salt bridges: D:K.171 SO4.19: 6 residues within 4Å: Chain B: R.71, L.226, M.248, W.419, L.420, S.421 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.421 Salt bridges: B:R.71 SO4.20: 4 residues within 4Å: Chain B: W.489, Y.494 Chain C: K.171, Q.175 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.175 Salt bridges: C:K.171 SO4.29: 6 residues within 4Å: Chain C: R.71, L.226, M.248, W.419, L.420, S.421 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.421 Salt bridges: C:R.71 SO4.30: 4 residues within 4Å: Chain B: K.171, Q.175 Chain C: W.489, Y.494 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.175, C:Y.494 Salt bridges: B:K.171 SO4.39: 6 residues within 4Å: Chain D: R.71, L.226, M.248, W.419, L.420, S.421 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.421 Salt bridges: D:R.71 SO4.40: 4 residues within 4Å: Chain A: K.171, Q.175 Chain D: W.489, Y.494 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.175, D:Y.494 Salt bridges: A:K.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, Y. et al., Crystal Structure of the Commercial Herbicide, Amidosulfuron, in Complex with Arabidopsis thaliana Acetohydroxyacid Synthase. J.Agric.Food Chem. (2023)

Release Date

2023-03-29

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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