MolNFT v1 · #121599 · protein
Prefusion structure of a human coronavirus spike protein
5I08 · Spike GLYCOPROTEIN,FOLDON chimera: “Prefusion structure of a human coronavirus spike protein”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #121599 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I08
- Type
- protein
- Length
- 2,874 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FOLDON chimera
- UniProt
- Q0ZME7, P10104
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike GLYCOPROTEIN,FOLDON chimera | protein | 958 | 25% helix, 27% strand | Q0ZME7, P10104 |
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 | 1002 | 0.87 | 0.88 | 116 | empty |
| 2 | 821 | 0.83 | 0.86 | 99 | empty |
| 3 | 212 | 0.82 | 0.95 | 40 | empty |
| 4 | 203 | 0.82 | 0.95 | 37 | empty |
| 5 | 211 | 0.82 | 0.95 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4016 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 4013 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 4013 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide (disulfide).
Compared structures
- 5I08 · Prefusion structure of a human coronavirus spike protein · 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 Q0ZME7
- Every structure of UniProt P10104
- Elsewhere: RCSB PDB 5I08 · PDBe 5I08 · UniProt Q0ZME7 · UniProt P10104
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