MolNFT v2 · #225179 · protein
Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-up state)
8XLM: “Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-up state)”. Electron microscopy at 3.22, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.87). MolNFT v2 #225179 on GenesisL1: 3D structure…
- PDB
- 8XLM
- Type
- protein
- Length
- 3,529 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.22
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Processed angiotensin-converting enzyme 2
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.22 · 4 distinct chains · 25% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 997 | 19% helix, 24% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 996 | 19% helix, 26% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 940 | 21% helix, 26% strand | P0DTC2 |
| D | Processed angiotensin-converting enzyme 2 | protein | 596 | 54% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 53 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains D
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 | 1011 | 0.87 | 0.88 | 102 | empty |
| 2 | 665 | 0.84 | 0.88 | 83 | empty |
| 3 | 1038 | 0.81 | 0.82 | 134 | empty |
| 4 | 941 | 0.80 | 0.82 | 79 | empty |
| 5 | 100 | 0.78 | 0.97 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4791 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4449 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 4050 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 834 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain D against A, TM-score 0.97
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
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 8XLM · PDBe 8XLM · UniProt P0DTC2 · UniProt Q9BYF1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.