MolNFT v2 · #220829 · protein
Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus SZ3 in Closed Conformation
8TC5: “Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus SZ3 in Closed Conformation”. Electron microscopy at 2.11, 5 ligands (EIC, NAG, FUC), 20 pockets (best druggability 0.84). MolNFT v2 #220829 on GenesisL1: 3D structure…
- PDB
- 8TC5
- Type
- protein
- Length
- 3,261 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.11
- Source
- Civet SARS CoV SZ3/2003
- Molecule
- Spike glycoprotein
- Ligands
- EIC, NAG, FUC, BMA, MAN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 2.11 · 1 distinct chain · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1087 | 23% helix, 33% strand | — |
Ligands and binding sites
- EIC · Linoleic acid · ligand · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 26 copies · chains C, A, B
- BMA · beta-D-mannopyranose · sugar · 21 copies
- MAN · alpha-D-mannopyranose · sugar · 6 copies
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 | 365 | 0.84 | 0.93 | 43 | EIC |
| 2 | 526 | 0.84 | 0.90 | 72 | empty |
| 3 | 428 | 0.84 | 0.91 | 60 | empty |
| 4 | 356 | 0.83 | 0.92 | 43 | EIC |
| 5 | 366 | 0.83 | 0.92 | 46 | EIC |
Interfaces
3 interfaces between chains.
- B–C · 6177 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 6176 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 6156 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 45 glycan (disulfide, N-glycosylation).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8TC5 · PDBe 8TC5
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