MolNFT v2 · #211268 · protein
cryo-EM structure of Omicron BA.5 S protein in complex with XGv282
8GTO · Spike glycoprotein: “cryo-EM structure of Omicron BA.5 S protein in complex with XGv282”. Electron microscopy at 3.2, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v2 #211268 on GenesisL1: 3D structure, binding sites…
- PDB
- 8GTO
- Type
- protein
- Length
- 3,759 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; heavy chain of XGv282; light chain of XGv282
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.2 · 3 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1025 | 19% helix, 31% strand | P0DTC2 |
| H, I, J | heavy chain of XGv282 | protein | 117 | 0% helix, 41% strand | — |
| L, M, N | light chain of XGv282 | protein | 111 | 0% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 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 | 774 | 0.87 | 0.90 | 92 | empty |
| 2 | 637 | 0.85 | 0.89 | 74 | empty |
| 3 | 982 | 0.81 | 0.82 | 81 | empty |
| 4 | 831 | 0.81 | 0.84 | 85 | empty |
| 5 | 1144 | 0.81 | 0.82 | 93 | empty |
Interfaces
17 interfaces between chains.
- A–C · 4746 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4631 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 4334 Ų buried · 26 hydrogen bonds · protein-protein
- I–M · 897 Ų buried · 4 hydrogen bonds · protein-protein
- J–N · 895 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 38 disulfide (N-glycosylation, disulfide).
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 8GTO · PDBe 8GTO · UniProt P0DTC2
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