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Crystal structure of arabidopsis thaliana acetohydroxyacid synthase in complex with a pyrimidinyl-benzoate herbicide, pyrithiobac
Analyse Crystal structure of arabidopsis thaliana acetohydroxyacid synthase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K2O
- Type
- protein
- Length
- 585 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetolactate synthase, chloroplastic
- EC
- 2.2.1.6
- UniProt
- P17597
- Ligands
- FAD, 6QK, TP9, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetolactate synthase, chloroplastic (EC 2.2.1.6) | protein | 585 | 41% helix, 16% strand | P17597 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- 6QK · 2-chloranyl-6-(4,6-dimethoxypyrimidin-2-yl)sulfanyl-benzoic acid · ligand · chains A
- TP9 · (3Z)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl]amino}-3-mercaptopent-3-en-1-yl trihydrogen diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.79 | 0.85 | 63 | FAD, 6QK |
| 2 | 59 | 0.52 | 0.87 | 22 | MG, TP9 |
| 3 | 62 | 0.39 | 0.80 | 18 | empty |
| 4 | 109 | 0.38 | 0.75 | 20 | empty |
| 5 | 74 | 0.32 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5K2O · Crystal structure of Arabidopsis thaliana acetohydroxyacid synthase in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P17597 · AlphaFold monomer V2.0 prediction for acetolactate synthase, chloroplastic (P17597) · 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 P17597
- Elsewhere: RCSB PDB 5K2O · PDBe 5K2O · UniProt P17597
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