Research workbench
Crystal structure of ketol-acid reductoisomerase from azotobacter
Analyse Crystal structure of ketol-acid reductoisomerase from azotobacter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XIY
- Type
- protein
- Length
- 1,312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketol-acid reductoisomerase
- EC
- 1.1.1.86
- UniProt
- C1DFH7
- Ligands
- MG, FE
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ketol-acid reductoisomerase (EC 1.1.1.86) | protein | 328 | 61% helix, 12% strand | C1DFH7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B, C, D
- PG4 · Tetraethylene glycol · additive · chains C, D
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 | 554 | 0.78 | 0.84 | 53 | FE, MG |
| 2 | 545 | 0.77 | 0.84 | 52 | FE |
| 3 | 624 | 0.77 | 0.83 | 53 | FE, MG |
| 4 | 572 | 0.77 | 0.83 | 47 | FE |
| 5 | 164 | 0.44 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 5854 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 5782 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 577 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 63 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4XIY · Crystal structure of ketol-acid reductoisomerase from Azotobacter · the same entry in another collection · chain A against A, TM-score 1.00
- C1DFH7 · AlphaFold monomer V2.0 prediction for ketol-acid reductoisomerase (NADP(+)) (C1DFH7) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 C1DFH7
- Elsewhere: RCSB PDB 4XIY · PDBe 4XIY · UniProt C1DFH7
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