Research workbench
Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein
Analyse Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TEY
- Type
- protein
- Length
- 2,703 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 2.25 · 2 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 834 | 24% helix, 36% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1035 | 21% helix, 34% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 56 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.86 | 0.88 | 129 | empty |
| 2 | 684 | 0.86 | 0.90 | 86 | empty |
| 3 | 527 | 0.81 | 0.87 | 66 | empty |
| 4 | 412 | 0.77 | 0.86 | 54 | empty |
| 5 | 582 | 0.74 | 0.82 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4641 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 4203 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 4177 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 glycan, 34 disulfide (N-glycosylation, disulfide).
Compared structures
- 7TEY · Cryo-EM structure of SARS-cov-2 delta (B.1.617.2) spike protein · 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 7TEY · PDBe 7TEY · UniProt P0DTC2
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