MolNFT v1 · #51719 · protein
Alditol oxidase from streptomyces coelicolor A3(2): complex with sorbitol
2VFT · Xylitol oxidase: “Alditol oxidase from streptomyces coelicolor A3(2): complex with sorbitol”. X-ray diffraction, 3 ligands (FAD, SOR, CL), 4 pockets (best druggability 0.84). MolNFT v1 #51719 on GenesisL1: 3D structure, binding…
- PDB
- 2VFT
- Type
- protein
- Length
- 415 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylitol oxidase
- EC
- 1.1.3.41
- UniProt
- Q9ZBU1
- Ligands
- FAD, SOR, CL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylitol oxidase (EC 1.1.3.41) | protein | 415 | 26% helix, 26% strand | Q9ZBU1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- SOR · sorbitol · ligand · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.84 | 0.89 | 78 | FAD, SOR |
| 2 | 56 | 0.35 | 0.79 | 18 | empty |
| 3 | 68 | 0.34 | 0.76 | 17 | empty |
| 4 | 87 | 0.34 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 2VFT · Alditol Oxidase from Streptomyces coelicolor A3(2): Complex with Sorbitol · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZBU1 · AlphaFold monomer V2.0 prediction for probable xylitol oxidase (Q9ZBU1) · 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 Q9ZBU1
- Elsewhere: RCSB PDB 2VFT · PDBe 2VFT · UniProt Q9ZBU1
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