MolNFT v1 · #179316 · protein
The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion.
7K1S · Envelope glycoprotein B: “The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion.”. Electron microscopy, 2 ligands (MAN, NAG), 19 pockets (best druggability 0.84). MolNFT v1 #179316 on GenesisL1: 3D…
- PDB
- 7K1S
- Type
- protein
- Length
- 1,752 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein B
- UniProt
- A0A076N502
- Ligands
- MAN, NAG
- Pockets
- 19 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope glycoprotein B | protein | 584 | 19% helix, 38% strand | A0A076N502 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.84 | 0.85 | 124 | empty |
| 2 | 125 | 0.80 | 0.97 | 27 | empty |
| 3 | 711 | 0.69 | 0.77 | 61 | empty |
| 4 | 673 | 0.69 | 0.77 | 54 | empty |
| 5 | 713 | 0.69 | 0.77 | 58 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6617 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 6587 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 6587 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7K1S · The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion. · 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 A0A076N502
- Elsewhere: RCSB PDB 7K1S · PDBe 7K1S · UniProt A0A076N502
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