Research workbench
Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), Cleavable form, one RBD-up conformation
Analyse Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), Cleavable form, one… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V8C
- Type
- protein
- Length
- 3,088 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.4 · 3 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1026 | 21% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1032 | 22% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1030 | 21% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 75 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 | 1146 | 0.87 | 0.88 | 147 | empty |
| 2 | 816 | 0.83 | 0.85 | 86 | empty |
| 3 | 1100 | 0.82 | 0.83 | 112 | empty |
| 4 | 423 | 0.79 | 0.88 | 46 | empty |
| 5 | 752 | 0.79 | 0.83 | 39 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4483 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 4359 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3864 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 7V8C · Cryo-EM structure of SARS-cov-2 S-beta variant (B.1.351), cleavable form, one rbd-up… · 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 7V8C · PDBe 7V8C · UniProt P0DTC2
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