Research workbench
Crystal structure of dimeric xylose reductase in complex with NADP(H)
Analyse Crystal structure of dimeric xylose reductase in complex with NADP(H) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K8C
- Type
- protein
- Length
- 1,274 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Candida tenuis
- Molecule
- xylose reductase
- EC
- 1.1.1.21
- UniProt
- O74237
- Ligands
- NAP
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | xylose reductase (EC 1.1.1.21) | protein | 317 | 40% helix, 15% strand | O74237 |
| B, C, D | xylose reductase (EC 1.1.1.21) | protein | 319 | 40% helix, 15% strand | O74237 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.73 | 0.78 | 81 | empty |
| 2 | 295 | 0.72 | 0.85 | 46 | NAP |
| 3 | 314 | 0.71 | 0.84 | 49 | NAP |
| 4 | 336 | 0.71 | 0.83 | 40 | NAP |
| 5 | 364 | 0.69 | 0.81 | 43 | NAP |
Interfaces
3 interfaces between chains.
- A–B · 1307 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1281 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 408 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1K8C · Crystal structure of dimeric xylose reductase in complex with NADP(H) · 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 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 O74237
- Elsewhere: RCSB PDB 1K8C · PDBe 1K8C · UniProt O74237
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