Research workbench
Crystal structure of the lys-274 to arg mutant of candida tenuis xylose reductase (AKR2B5) bound to NADP+
Analyse Crystal structure of the lys-274 to arg mutant of candida tenuis xylose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YE6
- Type
- protein
- Length
- 1,276 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H-dependent D-xylose reductase
- EC
- 1.1.1.-
- UniProt
- O74237
- Ligands
- NAP, NAD, SO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NAD(P)H-dependent D-xylose reductase (EC 1.1.1.-) | protein | 319 | 40% helix, 15% strand | O74237 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, C
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.75 | 0.85 | 49 | NAP |
| 2 | 361 | 0.74 | 0.85 | 48 | NAP |
| 3 | 312 | 0.71 | 0.84 | 43 | NAD |
| 4 | 308 | 0.70 | 0.83 | 42 | NAD |
| 5 | 448 | 0.65 | 0.78 | 48 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1274 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1267 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 122 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1YE6 · Crystal structure of the Lys-274 to Arg mutant of Candida tenuis xylose reductase… · the same entry in another collection · chain A against A, TM-score 1.00
- O74237 · AlphaFold monomer V2.0 prediction for NAD(P)H-dependent D-xylose reductase (O74237) · 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 O74237
- Elsewhere: RCSB PDB 1YE6 · PDBe 1YE6 · UniProt O74237
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