Research workbench
Crystal structure of staphylococcus aureus ketol-acid reductoisomerase with hydroxyoxamate inhibitor 2
Analyse Crystal structure of staphylococcus aureus ketol-acid reductoisomerase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BUL
- Type
- protein
- Length
- 648 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, E9G, E9J, MG
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 321 | 60% helix, 12% strand | Q2YUF3 |
| B | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 327 | 57% helix, 12% strand | Q2YUF3 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- E9G · {hydroxy[(1S)-1-phenylethyl]amino}(oxo)acetic acid · ligand · 2 copies · chains A, B
- E9J · oxo{[(1S)-1-phenylethyl]amino}acetic acid · ligand · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.78 | 0.86 | 55 | E9G, E9J, MG, NAP |
| 2 | 459 | 0.76 | 0.85 | 56 | MG, NAP, E9G, E9J |
| 3 | 86 | 0.69 | 0.93 | 22 | empty |
| 4 | 335 | 0.56 | 0.75 | 52 | empty |
| 5 | 70 | 0.32 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 5986 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 6BUL · Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase 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 6BUL · PDBe 6BUL · UniProt Q2YUF3
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