Research workbench
Cryo-EM structure of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement at downRBD conformation.
Analyse Cryo-EM structure of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8T25
- Type
- protein
- Length
- 787 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.62
- Source
- Neovison vison; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Angiotensin-converting enzyme; Spike glycoprotein
- UniProt
- A0A7T0Q2W2, P0DTC2
- Pockets
- 13 · best druggability 0.77
Structure
electron microscopy · resolution 3.62 · 2 distinct chains · 48% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme | protein | 595 | 60% helix, 2% strand | A0A7T0Q2W2 |
| B | Spike glycoprotein | protein | 192 | 11% helix, 19% strand | P0DTC2 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.77 | 0.89 | 37 | empty |
| 2 | 768 | 0.76 | 0.80 | 76 | empty |
| 3 | 777 | 0.70 | 0.76 | 68 | empty |
| 4 | 61 | 0.69 | 0.96 | 22 | empty |
| 5 | 77 | 0.60 | 0.88 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 925 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (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 A0A7T0Q2W2
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 8T25 · PDBe 8T25 · UniProt A0A7T0Q2W2 · UniProt P0DTC2
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