Research workbench
Holo structure of ketol-acid reductoisomerase from ignisphaera aggregans
Analyse Holo structure of ketol-acid reductoisomerase from ignisphaera aggregans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XDZ
- Type
- protein
- Length
- 657 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
- E0SRA9
- Ligands
- NDP, 40E, MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketol-acid reductoisomerase (EC 1.1.1.86) | protein | 328 | 60% helix, 12% strand | E0SRA9 |
| B | Ketol-acid reductoisomerase (EC 1.1.1.86) | protein | 329 | 60% helix, 12% strand | E0SRA9 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 40E · oxo(propan-2-ylamino)acetic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.76 | 0.85 | 53 | NDP, MG, 40E |
| 2 | 389 | 0.75 | 0.85 | 52 | NDP, MG, 40E |
| 3 | 181 | 0.46 | 0.75 | 28 | empty |
| 4 | 141 | 0.43 | 0.75 | 20 | empty |
| 5 | 71 | 0.39 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 6546 Ų buried · 66 hydrogen bonds · protein-protein
Compared structures
- 4XDZ · Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans · the same entry in another collection · chain A against A, TM-score 1.00
- E0SRA9 · AlphaFold monomer V2.0 prediction for ketol-acid reductoisomerase (NAD(P)(+)) (E0SRA9) · 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 E0SRA9
- Elsewhere: RCSB PDB 4XDZ · PDBe 4XDZ · UniProt E0SRA9
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