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Acetolactate synthase from klebsiella pneumoniae in complex with mechanism-based inhibitor
Analyse Acetolactate synthase from klebsiella pneumoniae in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6R
- Type
- protein
- Length
- 1,101 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetolactate synthase, catabolic
- EC
- 2.2.1.6
- UniProt
- P27696
- Ligands
- EN0, MG, PO4
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Acetolactate synthase, catabolic (EC 2.2.1.6) | protein | 548 | 44% helix, 19% strand | P27696 |
| M | Acetolactate synthase, catabolic (EC 2.2.1.6) | protein | 553 | 43% helix, 19% strand | P27696 |
Ligands and binding sites
- EN0 · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-[(Z)-2-fluoro-1-hydroxy-2-phosphonoethenyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1, 3-thiazol-3-ium · ligand · 2 copies · chains B, M
- MG · Magnesium ion · metal · 5 copies · chains B, M
- PO4 · Phosphate ion · ion · 2 copies · chains B, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.67 | 0.79 | 60 | empty |
| 2 | 437 | 0.67 | 0.79 | 65 | empty |
| 3 | 461 | 0.65 | 0.78 | 43 | empty |
| 4 | 364 | 0.62 | 0.78 | 55 | empty |
| 5 | 278 | 0.58 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- B–M · 177 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5D6R · Acetolactate Synthase from Klebsiella pneumoniae in Complex with Mechanism-Based Inhibitor · the same entry in another collection · chain B against B, TM-score 1.00
- P27696 · AlphaFold monomer V2.0 prediction for acetolactate synthase, catabolic (P27696) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P27696
- Elsewhere: RCSB PDB 5D6R · PDBe 5D6R · UniProt P27696
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