Research workbench
Acetolactate synthase from klebsiella pneumoniae in complex with a reaction intermediate
Analyse Acetolactate synthase from klebsiella pneumoniae in complex with a reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WDG
- Type
- protein
- Length
- 1,092 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
- A4Y, PYR, MG, PO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetolactate synthase, catabolic (EC 2.2.1.6) | protein | 538 | 45% helix, 19% strand | P27696 |
| B | Acetolactate synthase, catabolic (EC 2.2.1.6) | protein | 554 | 44% helix, 19% strand | P27696 |
Ligands and binding sites
- A4Y · (2S,3S)-2,3-dihydroxy-3-[(7s,8r,9as)-8-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2,7-dimethyl-5,7,8,10-tetrahydro-9AH-pyrimido[4,5-D][1, 3]thiazolo[3,2-a]pyrimidin-9A-yl]-2-methylbutanoic acid · ligand · 2 copies · chains A, B
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.70 | 0.80 | 69 | empty |
| 2 | 414 | 0.66 | 0.79 | 60 | empty |
| 3 | 370 | 0.60 | 0.77 | 54 | empty |
| 4 | 216 | 0.55 | 0.78 | 25 | empty |
| 5 | 193 | 0.54 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WDG · Acetolactate Synthase from Klebsiella pneumoniae in Complex with a Reaction Intermediate · the same entry in another collection · chain A against A, TM-score 1.00
- P27696 · AlphaFold monomer V2.0 prediction for acetolactate synthase, catabolic (P27696) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 5WDG · PDBe 5WDG · UniProt P27696
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