Research workbench
Structure of NADH-preferring ketol-acid reductoisomerase from an uncultured archean
Analyse Structure of NADH-preferring ketol-acid reductoisomerase from an uncultured… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XDY
- Type
- protein
- Length
- 662 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketol-acid reductoisomerase
- EC
- 1.1.1.86
- UniProt
- Q64BR7
- Ligands
- NAI, HIO, MG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ketol-acid reductoisomerase (EC 1.1.1.86) | protein | 331 | 60% helix, 14% strand | Q64BR7 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- HIO · N-hydroxy-N-isopropyloxamic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.75 | 0.85 | 47 | HIO, MG, NAI |
| 2 | 347 | 0.74 | 0.86 | 46 | MG, NAI, HIO |
| 3 | 169 | 0.52 | 0.78 | 30 | empty |
| 4 | 75 | 0.38 | 0.77 | 14 | empty |
| 5 | 62 | 0.36 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 6222 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 4XDY · Structure of NADH-preferring ketol-acid reductoisomerase from an uncultured archean · the same entry in another collection · chain A against A, TM-score 1.00
- Q64BR7 · AlphaFold monomer V2.0 prediction for ketol-acid reductoisomerase (NAD(+)) (Q64BR7) · 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 Q64BR7
- Elsewhere: RCSB PDB 4XDY · PDBe 4XDY · UniProt Q64BR7
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