MolNFT v2 · #226651 · protein
SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5.1)
9AYX · Spike glycoprotein: “SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5.1)”. Electron microscopy at 3.0, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v2 #226651 on GenesisL1: 3D…
- PDB
- 9AYX
- Type
- protein
- Length
- 3,123 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.0 · 1 distinct chain · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1041 | 22% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 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 | 896 | 0.86 | 0.88 | 118 | empty |
| 2 | 606 | 0.85 | 0.90 | 87 | empty |
| 3 | 920 | 0.85 | 0.86 | 104 | empty |
| 4 | 855 | 0.84 | 0.86 | 99 | empty |
| 5 | 434 | 0.83 | 0.91 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6337 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 6284 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 6266 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 30 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
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 9AYX · PDBe 9AYX · UniProt P0DTC2
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