Research workbench
Crystal structures of staphylococcus aureus ketol-acid reductoisomerase in complex with two transition state analogs that have biocidal activity.
Analyse Crystal structures of staphylococcus aureus ketol-acid reductoisomerase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AQJ
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketol-acid reductoisomerase (NADP(+))
- EC
- 1.1.1.86
- UniProt
- Q2YUF3
- Ligands
- 40E, NDP, HIO, MG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 326 | 60% helix, 12% strand | Q2YUF3 |
Ligands and binding sites
- 40E · oxo(propan-2-ylamino)acetic acid · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- HIO · N-hydroxy-N-isopropyloxamic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.75 | 0.85 | 50 | 40E, HIO, MG, NDP |
| 2 | 446 | 0.73 | 0.83 | 56 | MG, 40E, GOL, NDP, HIO |
| 3 | 105 | 0.55 | 0.84 | 20 | empty |
| 4 | 211 | 0.50 | 0.76 | 27 | GOL |
| 5 | 68 | 0.34 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 6307 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 6AQJ · Crystal structures of Staphylococcus aureus ketol-acid reductoisomerase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2YUF3 · AlphaFold monomer V2.0 prediction for ketol-acid reductoisomerase (NADP(+)) (Q2YUF3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q2YUF3
- Elsewhere: RCSB PDB 6AQJ · PDBe 6AQJ · UniProt Q2YUF3
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