MolNFT v1 · #144806 · protein
Crystal structure of staphylococcus aureus ketol-acid reductosimerrase with hydroxyoxamate inhibitor 3
6C55 · Ketol-acid reductoisomerase (NADP(+)): “Crystal structure of staphylococcus aureus ketol-acid reductosimerrase with hydroxyoxamate inhibitor 3”. X-ray diffraction, 4 ligands (NAP, EKD, EKA), 6 pockets (best druggability 0.77).…
- PDB
- 6C55
- 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
- NAP, EKD, EKA, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 326 | 59% helix, 12% strand | Q2YUF3 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- EKD · (cyclohexylamino)(oxo)acetic acid · ligand · 2 copies · chains A, B
- EKA · [cyclohexyl(hydroxy)amino](oxo)acetic acid · ligand · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.77 | 0.86 | 58 | MG, EKD, NAP |
| 2 | 458 | 0.76 | 0.84 | 55 | MG, NAP, EKD, EKA |
| 3 | 136 | 0.70 | 0.90 | 24 | empty |
| 4 | 52 | 0.64 | 0.94 | 16 | empty |
| 5 | 331 | 0.57 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 6320 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 6C55 · Crystal structure of Staphylococcus aureus Ketol-acid Reductosimerrase 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 6C55 · PDBe 6C55 · UniProt Q2YUF3
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