MolNFT v1 · #188205 · protein
Omicron spike at 3.0 a (open form)
7TGW · Spike glycoprotein: “Omicron spike at 3.0 a (open form)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #188205 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TGW
- Type
- protein
- Length
- 3,307 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 0.87
Structure
electron microscopy · 3 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1113 | 19% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1091 | 19% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1103 | 20% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 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 | 1087 | 0.87 | 0.88 | 120 | empty |
| 2 | 805 | 0.86 | 0.88 | 67 | empty |
| 3 | 1039 | 0.85 | 0.86 | 116 | empty |
| 4 | 857 | 0.84 | 0.86 | 97 | empty |
| 5 | 868 | 0.84 | 0.86 | 94 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5636 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 5537 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 4488 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 27 glycan (disulfide, N-glycosylation).
Compared structures
- 7TGW · Omicron spike at 3.0 A (open form) · 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 7TGW · PDBe 7TGW · UniProt P0DTC2
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