MolNFT v2 · #223970 · protein
SARS-CoV-2 Omicron BQ.1 RBD complexed with human ACE2
8WDZ · Angiotensin-converting enzyme 2: “SARS-CoV-2 Omicron BQ.1 RBD complexed with human ACE2”. Electron microscopy at 2.71, 3 ligands (NAG, FUC, ZN), 4 pockets (best druggability 0.73). MolNFT v2 #223970 on GenesisL1: 3D structure…
- PDB
- 8WDZ
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.71
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, FUC, ZN
- Pockets
- 4 · best druggability 0.73
Structure
electron microscopy · resolution 2.71 · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 | protein | 596 | 59% helix, 3% strand | Q9BYF1 |
| B | Spike protein S1 | protein | 195 | 9% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.73 | 0.79 | 90 | empty |
| 2 | 315 | 0.66 | 0.81 | 36 | empty |
| 3 | 94 | 0.33 | 0.73 | 23 | empty |
| 4 | 51 | 0.26 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 862 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 8WDZ · PDBe 8WDZ · UniProt Q9BYF1 · UniProt P0DTC2
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