Research workbench
Rice ketolacid reductoisomerase in complex with MG2+-NADPH
Analyse Rice ketolacid reductoisomerase in complex with MG2+-NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FR8
- Type
- protein
- Length
- 1,018 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ketol-acid reductoisomerase (OS05G0573700 protein)
- EC
- 1.1.1.86
- UniProt
- Q65XK0
- Ligands
- NDP, MG, SO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ketol-acid reductoisomerase (OS05G0573700 protein) (EC 1.1.1.86) | protein | 501 | 56% helix, 11% strand | Q65XK0 |
| B | Putative ketol-acid reductoisomerase (OS05G0573700 protein) (EC 1.1.1.86) | protein | 517 | 54% helix, 10% strand | Q65XK0 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.78 | 0.97 | 26 | empty |
| 2 | 533 | 0.77 | 0.84 | 59 | MG, NDP, PEG |
| 3 | 112 | 0.76 | 0.96 | 26 | empty |
| 4 | 407 | 0.74 | 0.84 | 52 | NDP, PE4 |
| 5 | 147 | 0.65 | 0.87 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2332 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3FR8 · rice Ketolacid reductoisomerase in complex with Mg2+-NADPH · the same entry in another collection · chain A against A, TM-score 1.00
- Q65XK0 · AlphaFold monomer V2.0 prediction for ketol-acid reductoisomerase, chloroplastic (Q65XK0) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q65XK0
- Elsewhere: RCSB PDB 3FR8 · PDBe 3FR8 · UniProt Q65XK0
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