MolNFT v1 · #177170 · protein
Nanometer resolution in situ structure of SARS-cov-2 post-fusion spike
7E9T · Spike protein S2: “Nanometer resolution in situ structure of SARS-cov-2 post-fusion spike”. Electron microscopy, 2 ligands (NAG, MAN), 10 pockets (best druggability 0.78). MolNFT v1 #177170 on GenesisL1: 3D structure, binding sites…
- PDB
- 7E9T
- Type
- protein
- Length
- 1,113 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S2
- UniProt
- P0DTC2
- Ligands
- NAG, MAN
- Pockets
- 10 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike protein S2 | protein | 371 | 51% helix, 19% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.78 | 0.80 | 73 | empty |
| 2 | 817 | 0.75 | 0.80 | 69 | empty |
| 3 | 83 | 0.75 | 0.97 | 20 | empty |
| 4 | 80 | 0.73 | 0.97 | 17 | empty |
| 5 | 239 | 0.63 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6889 Ų buried · 86 hydrogen bonds · protein-protein
- B–C · 6889 Ų buried · 86 hydrogen bonds · protein-protein
- A–C · 6887 Ų buried · 87 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 7E9T · Nanometer resolution in situ structure of SARS-CoV-2 post-fusion spike · 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 7E9T · PDBe 7E9T · UniProt P0DTC2
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