MolNFT v1 · #171778 · protein
Uncleavable spike protein of SARS-cov-2 in closed conformation
6ZGE · Spike glycoprotein: “Uncleavable spike protein of SARS-cov-2 in closed conformation”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #171778 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6ZGE
- Type
- protein
- Length
- 3,294 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1098 | 21% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 81 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.88 | 0.89 | 124 | empty |
| 2 | 749 | 0.86 | 0.90 | 98 | empty |
| 3 | 291 | 0.85 | 0.95 | 36 | empty |
| 4 | 669 | 0.84 | 0.88 | 92 | empty |
| 5 | 297 | 0.84 | 0.94 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6409 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 6404 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 6404 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZGE · Uncleavable Spike Protein of SARS-CoV-2 in Closed Conformation · 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 P0DTC2
- Elsewhere: RCSB PDB 6ZGE · PDBe 6ZGE · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.