MolNFT v1 · #36444 · protein
Reaction geometry and thermostability mutant of pyranose 2-oxidase from the white-rot fungus peniophora sp.
2F5V: “Reaction geometry and thermostability mutant of pyranose 2-oxidase from the white-rot fungus peniophora sp.”. X-ray diffraction, 2 ligands (KBG, FAD), 5 pockets (best druggability 0.88). MolNFT v1 #36444 on GenesisL1: 3D structure…
- PDB
- 2F5V
- Type
- protein
- Length
- 577 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyranose 2-oxidase
- EC
- 1.1.3.10
- UniProt
- Q8J136
- Ligands
- KBG, FAD
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyranose 2-oxidase (EC 1.1.3.10) | protein | 577 | 24% helix, 23% strand | Q8J136 |
Ligands and binding sites
- KBG · beta-D-arabino-hexopyranos-2-ulose · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.88 | 0.94 | 67 | KBG, FAD |
| 2 | 395 | 0.67 | 0.80 | 52 | empty |
| 3 | 94 | 0.52 | 0.83 | 21 | empty |
| 4 | 89 | 0.37 | 0.76 | 20 | empty |
| 5 | 59 | 0.32 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 2F5V · Reaction geometry and thermostability mutant of pyranose 2-oxidase from the white-rot… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8J136 · AlphaFold monomer V2.0 prediction for pyranose 2-oxidase (Q8J136) · a predicted model of the same protein · chain A 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 Q8J136
- Elsewhere: RCSB PDB 2F5V · PDBe 2F5V · UniProt Q8J136
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