Research workbench
Structure of L-xylulose reductase with bound coenzyme, phosphate and hydroxide.
Analyse Structure of L-xylulose reductase with bound coenzyme, phosphate and hydroxide. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D3W
- Type
- protein
- Length
- 488 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-xylulose reductase
- EC
- 1.1.1.10
- UniProt
- Q7Z4W1
- Ligands
- NAP, PO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-xylulose reductase (EC 1.1.1.10) | protein | 244 | 48% helix, 17% strand | Q7Z4W1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.76 | 0.86 | 45 | NAP, PO4 |
| 2 | 355 | 0.76 | 0.86 | 43 | NAP |
| 3 | 320 | 0.55 | 0.75 | 33 | empty |
| 4 | 51 | 0.29 | 0.75 | 11 | empty |
| 5 | 52 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 292 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, oxidation).
Compared structures
- 3D3W · Structure of L-Xylulose Reductase with bound coenzyme, phosphate and hydroxide. · the same entry in another collection · chain A against A, TM-score 1.00
- Q7Z4W1 · AlphaFold monomer V2.0 prediction for L-xylulose reductase (Q7Z4W1) · a predicted model of the same protein · chain B 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 Q7Z4W1
- Elsewhere: RCSB PDB 3D3W · PDBe 3D3W · UniProt Q7Z4W1
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