SMTL ID : 5wkc.1 (1 other biounit)

Saccharomyces cerevisiae acetohydroxyacid synthase in complex with the herbicide penoxsulam

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.540, N.567, E.569, G.571 Ligands: AUJ.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.540, A:E.569, H2O.2 MG.6: 5 residues within 4Å: Chain B: D.540, N.567, E.569, G.571 Ligands: TP9.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.540, B:E.569, H2O.15

2 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.2: 16 residues within 4Å: Chain A: M.344, D.369, R.370, M.572, V.573, W.576 Chain B: G.106, A.107, L.109, S.153, V.181, A.190, F.191, K.241 Ligands: FAD.3, AUJ.5 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.181, B:A.190 Hydrogen bonds: B:K.241, B:K.241, A:R.370, A:R.370 Halogen bonds: B:S.153 pi-Stacking: A:W.576, A:W.576, A:W.576 PXD.7: 17 residues within 4Å: Chain A: G.106, A.107, L.109, S.153, V.181, P.182, A.190, F.191, K.241 Chain B: M.344, D.369, R.370, M.572, V.573, W.576 Ligands: F50.4, FAD.8 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.370, B:R.370, A:K.241, A:K.241 pi-Stacking: B:W.576, B:W.576, B:W.576 Hydrophobic interactions: A:V.181, A:A.190 Halogen bonds: A:S.153

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

FAD.3: 37 residues within 4Å: Chain A: D.170, R.231, G.297, A.298, G.299, N.302, T.324, L.325, Q.326, M.341, L.342, G.343, M.344, H.345, G.346, G.364, A.365, R.366, D.368, R.370, V.371, F.396, E.397, V.398, N.402, G.415, D.416, A.417, V.487, Q.491, M.492, S.509, G.510, G.511, M.572 Chain B: F.191 Ligands: PXD.2 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.325, A:V.487, B:F.191 Hydrogen bonds: A:R.231, A:A.298, A:N.302, A:T.324, A:T.324, A:L.325, A:L.342, A:H.345, A:R.366, A:V.398, A:N.402, A:D.416, A:D.416, A:A.417, A:G.510 Water bridges: A:R.231, A:R.231, A:Q.326, A:G.364, A:R.366, A:R.366, A:F.367, A:T.418 Salt bridges: A:R.231, A:R.366 FAD.8: 38 residues within 4Å: Chain A: F.191 Chain B: A.169, D.170, R.231, G.297, A.298, G.299, N.302, T.324, L.325, Q.326, L.342, G.343, M.344, H.345, G.346, G.364, A.365, R.366, D.368, R.370, V.371, F.396, E.397, V.398, S.399, N.402, G.415, D.416, A.417, V.487, Q.491, M.492, S.509, G.510, G.511, M.572 Ligands: PXD.7 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.325, B:V.487, A:F.191 Hydrogen bonds: B:R.231, B:A.298, B:N.302, B:T.324, B:T.324, B:L.325, B:L.342, B:H.345, B:R.366, B:R.366, B:V.398, B:N.402, B:D.416, B:A.417, B:G.510 Water bridges: B:R.231, B:R.231, B:G.364, B:F.367, B:T.418 Salt bridges: B:R.231, B:R.366

1 x F50: ETHANEPEROXOIC ACID(Non-covalent)

F50.4: 7 residues within 4Å: Chain A: G.105, G.106, Q.192 Chain B: V.487, M.572 Ligands: PXD.7, TP9.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.106, A:Q.192 Water bridges: A:A.107 Hydrophobic interactions: B:M.572

1 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.5: 28 residues within 4Å: Chain A: V.487, G.488, Q.489, H.490, G.513, M.515, G.539, D.540, A.541, S.542, M.545, N.567, E.569, Q.570, G.571, M.572, V.573 Chain B: Y.103, P.104, G.105, G.106, E.129, T.152, P.155, N.159, Q.192 Ligands: MG.1, PXD.2 21 PLIP interactions: 6 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:Y.103, B:P.155, A:Q.570, A:V.573 Hydrogen bonds: B:G.106, B:Q.192, A:Q.489, A:Q.489, A:H.490, A:G.513, A:M.515, A:D.540, A:A.541, A:S.542, A:N.567, A:G.571, A:M.572 Water bridges: B:A.107, B:T.152 Salt bridges: A:H.490, A:H.490

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

TP9.9: 27 residues within 4Å: Chain A: Y.103, P.104, G.105, E.129, T.152, P.155, N.159, Q.192 Chain B: V.487, G.488, Q.489, H.490, G.513, M.515, G.539, D.540, A.541, S.542, M.545, N.567, E.569, Q.570, G.571, M.572, V.573 Ligands: F50.4, MG.6 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:Y.103, A:P.155, B:M.515, B:Q.570, B:V.573 Hydrogen bonds: B:Q.489, B:H.490, B:G.513, B:M.515, B:D.540, B:A.541, B:S.542, B:N.567, B:G.571, B:M.572 Salt bridges: B:H.490, B:H.490

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 catalytic subunit, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Acetolactate synthase catalytic subunit, mitochondrial

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