MolNFT v1 · #190623 · protein
SARS-cov-2 omicron BA.4 variant spike
7XNQ · Spike glycoprotein: “SARS-cov-2 omicron BA.4 variant spike”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #190623 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XNQ
- Type
- protein
- Length
- 3,267 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 · 1 distinct chain · 21% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1089 | 21% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 copies · chains A, C, B
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 | 1172 | 0.87 | 0.88 | 121 | empty |
| 2 | 1072 | 0.83 | 0.84 | 113 | empty |
| 3 | 1186 | 0.82 | 0.83 | 129 | empty |
| 4 | 507 | 0.81 | 0.87 | 44 | empty |
| 5 | 310 | 0.80 | 0.90 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5588 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 5544 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 5515 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 glycan, 36 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7XNQ · SARS-CoV-2 Omicron BA.4 variant spike · 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 7XNQ · PDBe 7XNQ · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.