MolNFT v1 · #171554 · protein
Structure of the prefusion SARS-cov-2 spike glycoprotein
6Z97 · Spike GLYCOPROTEIN,FIBRITIN: “Structure of the prefusion SARS-cov-2 spike glycoprotein”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #171554 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Z97
- Type
- protein
- Length
- 2,975 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN
- UniProt
- P0DTC2, P10104
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 995 | 23% helix, 31% strand | P0DTC2, P10104 |
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 989 | 24% helix, 32% strand | P0DTC2, P10104 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 991 | 24% helix, 32% strand | P0DTC2, P10104 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 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 | 808 | 0.87 | 0.90 | 102 | empty |
| 2 | 723 | 0.83 | 0.86 | 91 | empty |
| 3 | 449 | 0.82 | 0.89 | 55 | empty |
| 4 | 461 | 0.79 | 0.87 | 51 | empty |
| 5 | 340 | 0.75 | 0.86 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5085 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4642 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 4338 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 38 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z97 · Structure of the prefusion SARS-CoV-2 spike 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 P0DTC2
- Every structure of UniProt P10104
- Elsewhere: RCSB PDB 6Z97 · PDBe 6Z97 · UniProt P0DTC2 · UniProt P10104
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