MolNFT v1 · #138471 · protein
Saccharomyces cerevisiae acetohydroxyacid synthase in complex with the herbicide penoxsulam
5WKC · Acetolactate synthase catalytic subunit, mitochondrial: “Saccharomyces cerevisiae acetohydroxyacid synthase in complex with the herbicide penoxsulam”. X-ray diffraction, 6 ligands (PXD, FAD, F50), 20 pockets (best druggability…
- PDB
- 5WKC
- Type
- protein
- Length
- 2,377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetolactate synthase catalytic subunit, mitochondrial
- EC
- 2.2.1.6
- UniProt
- P07342
- Ligands
- PXD, FAD, F50, TP9, AUJ, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetolactate synthase catalytic subunit, mitochondrial (EC 2.2.1.6) | protein | 591 | 44% helix, 16% strand | P07342 |
| B | Acetolactate synthase catalytic subunit, mitochondrial (EC 2.2.1.6) | protein | 598 | 43% helix, 17% strand | P07342 |
| E | Acetolactate synthase catalytic subunit, mitochondrial (EC 2.2.1.6) | protein | 592 | 44% helix, 16% strand | P07342 |
| D | Acetolactate synthase catalytic subunit, mitochondrial (EC 2.2.1.6) | protein | 596 | 44% helix, 16% strand | P07342 |
Ligands and binding sites
- PXD · 2-(2,2-difluoroethoxy)-N-(5,8-dimethoxy[1,2, 4]triazolo[1,5-c]pyrimidin-2-yl)-6-(trifluoromethyl) benzenesulfonamide · ligand · 4 copies · chains A, D, B, E
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, D, B, E
- F50 · Ethaneperoxoic acid · ligand · 3 copies · chains A, D, B, E
- TP9 · (3Z)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl]amino}-3-mercaptopent-3-en-1-yl trihydrogen diphosphate · ligand · 3 copies · chains B, E, A, D
- 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 · ligand · chains A, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.86 | 0.89 | 117 | F50, MG, PXD, FAD, TP9 |
| 2 | 852 | 0.86 | 0.89 | 112 | MG, PXD, FAD, TP9, F50 |
| 3 | 926 | 0.86 | 0.87 | 113 | MG, PXD, FAD, AUJ |
| 4 | 948 | 0.86 | 0.87 | 117 | F50, MG, PXD, FAD, TP9 |
| 5 | 1155 | 0.79 | 0.80 | 91 | empty |
Interfaces
3 interfaces between chains.
- A–D · 3143 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 3140 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 876 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5WKC · Saccharomyces cerevisiae acetohydroxyacid synthase in complex with the herbicide… · the same entry in another collection · chain D against D, TM-score 1.00
- P07342 · AlphaFold monomer V2.0 prediction for acetolactate synthase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P07342
- Elsewhere: RCSB PDB 5WKC · PDBe 5WKC · UniProt P07342
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