MolNFT v1 · #172771 · protein
Cryo-EM structure of a prefusion stabilized SARS-cov-2 spike (D614N, R682S, R685G, A892P, A942P and V987P)(ONE up trimer)
7AD1 · Spike GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,SPIKE…: “Cryo-EM structure of a prefusion stabilized SARS-cov-2 spike (D614N, R682S, R685G, A892P, A942P and…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86).…
- PDB
- 7AD1
- Type
- protein
- Length
- 2,830 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,SPIKE GLYCOPROTEIN,ENVELOPE…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,SPIKE GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,SARS-cov-2 S protein | protein | 950 | 24% helix, 33% strand | P0DTC2 |
| B | Spike GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,SPIKE GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,SARS-cov-2 S protein | protein | 935 | 23% helix, 31% strand | P0DTC2 |
| C | Spike GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,SPIKE GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,SARS-cov-2 S protein | protein | 945 | 25% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C
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 | 756 | 0.86 | 0.90 | 95 | empty |
| 2 | 1037 | 0.84 | 0.85 | 133 | empty |
| 3 | 642 | 0.82 | 0.87 | 62 | empty |
| 4 | 813 | 0.82 | 0.84 | 92 | empty |
| 5 | 467 | 0.73 | 0.82 | 63 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4655 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 4316 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 3925 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 20 glycan (disulfide, N-glycosylation).
Compared structures
- 7AD1 · Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P… · 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 7AD1 · PDBe 7AD1 · UniProt P0DTC2
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