MolNFT v1 · #28750 · protein
Aldo-keto reductase AKR11C1 from bacillus halodurans (apo form)
1YNP · Oxidoreductase: “Aldo-keto reductase AKR11C1 from bacillus halodurans (apo form)”. X-ray diffraction, 4 ligands (GLC, FRU, NA), 6 pockets (best druggability 0.61). MolNFT v1 #28750 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1YNP
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase
- UniProt
- Q9KE47
- Ligands
- GLC, FRU, NA, SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase | protein | 283 | 42% helix, 18% strand | Q9KE47 |
| B | Oxidoreductase | protein | 298 | 41% helix, 19% strand | Q9KE47 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- NA · Sodium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.61 | 0.79 | 37 | GLC, FRU, SO4 |
| 2 | 334 | 0.56 | 0.76 | 40 | empty |
| 3 | 221 | 0.54 | 0.77 | 35 | NA, SO4 |
| 4 | 124 | 0.43 | 0.76 | 28 | SO4, GOL |
| 5 | 53 | 0.25 | 0.73 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 697 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1YNP · aldo-keto reductase AKR11C1 from Bacillus halodurans (apo form) · the same entry in another collection · chain A 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 Q9KE47
- Elsewhere: RCSB PDB 1YNP · PDBe 1YNP · UniProt Q9KE47
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