MolNFT v1 · #141418 · protein
Crystal structure of D-xylose reductase from scheffersomyces stipitis
5Z6U · NAD(P)H-dependent D-xylose reductase: “Crystal structure of D-xylose reductase from scheffersomyces stipitis”. X-ray diffraction, 6 pockets (best druggability 0.71). MolNFT v1 #141418 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Z6U
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H-dependent D-xylose reductase
- EC
- 1.1.1.307
- UniProt
- P31867
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD(P)H-dependent D-xylose reductase (EC 1.1.1.307) | protein | 318 | 40% helix, 15% strand | P31867 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 587 | 0.71 | 0.79 | 53 | empty |
| 2 | 301 | 0.65 | 0.81 | 45 | GOL |
| 3 | 204 | 0.59 | 0.81 | 24 | empty |
| 4 | 69 | 0.56 | 0.87 | 19 | empty |
| 5 | 103 | 0.47 | 0.79 | 21 | GOL |
Interfaces
1 interface between chains.
- A–B · 1381 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5Z6U · Crystal structure of D-xylose reductase from Scheffersomyces stipitis · the same entry in another collection · chain A against A, TM-score 1.00
- P31867 · AlphaFold monomer V2.0 prediction for NAD(P)H-dependent D-xylose reductase (P31867) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P31867
- Elsewhere: RCSB PDB 5Z6U · PDBe 5Z6U · UniProt P31867
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