Research workbench
Arabidopsis thaliana acetohydroxyacid synthase complex with valine bound
Analyse Arabidopsis thaliana acetohydroxyacid synthase complex with valine bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VZ8
- Type
- protein
- Length
- 5,560 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetolactate synthase, chloroplastic; Acetolactate synthase small subunit 2, chloroplastic
- EC
- 2.2.1.6
- UniProt
- P17597, Q93YZ7
- Ligands
- FAD, TPP, VAL, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, H, L, P | Acetolactate synthase, chloroplastic (EC 2.2.1.6) | protein | 531 | 41% helix, 16% strand | P17597 |
| E, I, M, Q | Acetolactate synthase, chloroplastic (EC 2.2.1.6) | protein | 541 | 41% helix, 17% strand | P17597 |
| F, J, N, R | Acetolactate synthase small subunit 2, chloroplastic | protein | 159 | 31% helix, 43% strand | Q93YZ7 |
| G, K, O, S | Acetolactate synthase small subunit 2, chloroplastic | protein | 159 | 30% helix, 40% strand | Q93YZ7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains D, E, H, I, L, M, P, Q
- TPP · Thiamine diphosphate · ligand · 8 copies · chains D, E, H, I, L, M, P, Q
- VAL · Valine · ligand · 8 copies · chains F, G, J, K, N, O, R, S
- MG · Magnesium ion · metal · 8 copies · chains D, E, H, I, L, M, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.88 | 0.91 | 113 | empty |
| 2 | 629 | 0.88 | 0.93 | 92 | empty |
| 3 | 930 | 0.88 | 0.90 | 116 | empty |
| 4 | 883 | 0.87 | 0.89 | 118 | MG, FAD, TPP |
| 5 | 825 | 0.86 | 0.89 | 102 | MG, FAD, TPP |
Interfaces
36 interfaces between chains.
- P–Q · 2737 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 2726 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 2719 Ų buried · 13 hydrogen bonds · protein-protein
- L–M · 2718 Ų buried · 13 hydrogen bonds · protein-protein
- R–S · 2412 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6VZ8 · Arabidopsis thaliana acetohydroxyacid synthase complex with valine bound · the same entry in another collection · chain K against K, 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
- Every structure of UniProt Q93YZ7
- Elsewhere: RCSB PDB 6VZ8 · PDBe 6VZ8 · UniProt P17597 · UniProt Q93YZ7
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