MolNFT v1 · #82364 · protein
Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase-mannose complex
3VKK: “Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase-mannose complex”. X-ray diffraction, 5 ligands (PLM, OLA, MAN), 1 pocket (best druggability 0.76). MolNFT v1 #82364 on GenesisL1: 3D structure…
- PDB
- 3VKK
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- Q9H227
- Ligands
- PLM, OLA, MAN, MG, CL
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic beta-glucosidase (EC 3.2.1.21) | protein | 466 | 45% helix, 18% strand | Q9H227 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- OLA · Oleic acid · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.76 | 0.83 | 47 | GOL, PLM, OLA, MAN |
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 3VKK · Crystal Structure Of The Covalent Intermediate Of Human Cytosolic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H227 · AlphaFold monomer V2.0 prediction for cytosolic beta-glucosidase (Q9H227) · 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 Q9H227
- Elsewhere: RCSB PDB 3VKK · PDBe 3VKK · UniProt Q9H227
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