MolNFT v1 · #178402 · protein
SARS-cov-2 B.1.1.7 spike glycoprotein trimer
7FET: “SARS-cov-2 B.1.1.7 spike glycoprotein trimer”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #178402 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7FET
- Type
- protein
- Length
- 3,003 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 0.86
Structure
electron microscopy · 3 distinct chains · 19% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1001 | 19% helix, 24% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 999 | 18% helix, 22% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1003 | 20% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 41 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 | 942 | 0.86 | 0.87 | 121 | empty |
| 2 | 533 | 0.85 | 0.91 | 68 | empty |
| 3 | 973 | 0.80 | 0.82 | 92 | empty |
| 4 | 660 | 0.80 | 0.85 | 76 | empty |
| 5 | 849 | 0.79 | 0.82 | 71 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4772 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 4520 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4206 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 33 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7FET · SARS-CoV-2 B.1.1.7 Spike Glycoprotein trimer · 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 7FET · PDBe 7FET · UniProt P0DTC2
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