MolNFT v1 · #167463 · protein
A varicella-zoster virus glycoprotein
6VLK · Envelope glycoprotein B: “A varicella-zoster virus glycoprotein”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 11 pockets (best druggability 0.51). MolNFT v1 #167463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VLK
- Type
- protein
- Length
- 1,167 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B
- UniProt
- Q4JR05
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein B | protein | 584 | 20% helix, 38% strand | Q4JR05 |
| B | Envelope glycoprotein B | protein | 583 | 20% helix, 38% strand | Q4JR05 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.51 | 0.77 | 28 | empty |
| 2 | 182 | 0.48 | 0.76 | 21 | empty |
| 3 | 153 | 0.45 | 0.76 | 21 | empty |
| 4 | 114 | 0.45 | 0.78 | 32 | empty |
| 5 | 144 | 0.44 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 341 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6VLK · A varicella-zoster virus glycoprotein · the same entry in another collection · 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 Q4JR05
- Elsewhere: RCSB PDB 6VLK · PDBe 6VLK · UniProt Q4JR05
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.