MolNFT v1 · #51721 · protein
Alditol oxidase from streptomyces coelicolor A3(2): complex with sulphite
2VFV · Xylitol oxidase: “Alditol oxidase from streptomyces coelicolor A3(2): complex with sulphite”. X-ray diffraction, 2 ligands (SFD, CL), 5 pockets (best druggability 0.85). MolNFT v1 #51721 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VFV
- Type
- protein
- Length
- 418 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
- SFD, CL
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylitol oxidase (EC 1.1.3.41) | protein | 418 | 26% helix, 25% strand | Q9ZBU1 |
Ligands and binding sites
- SFD · (S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl)methoxy)(hydroxy)phosphoryloxy)(hydroxy)phosphoryloxy)-2,3,4-trihydroxypentyl)-7,8-dimethyl-2,4-dioxo-2,3,4,4A-tetrahydrobenzo[g]pteridine-5(10H)-sulfonic acid · 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.85 | 0.91 | 77 | SFD |
| 2 | 98 | 0.37 | 0.75 | 23 | empty |
| 3 | 86 | 0.35 | 0.75 | 20 | empty |
| 4 | 52 | 0.34 | 0.78 | 18 | empty |
| 5 | 52 | 0.27 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2VFV · Alditol Oxidase from Streptomyces coelicolor A3(2): Complex with Sulphite · 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 2VFV · PDBe 2VFV · UniProt Q9ZBU1
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