MolNFT v2 · #227562 · protein
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Delta (B.1.617.2) variant 3 closed RBDs
9CRH · Spike glycoprotein: “Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Delta (B.1.617.2) variant 3 closed RBDs”. Electron microscopy at 3.4, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.87). MolNFT v2…
- PDB
- 9CRH
- Type
- protein
- Length
- 2,982 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, FUC
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.4 · 1 distinct chain · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Spike glycoprotein | protein | 994 | 23% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, 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 | 824 | 0.87 | 0.90 | 120 | empty |
| 2 | 483 | 0.85 | 0.92 | 70 | empty |
| 3 | 534 | 0.85 | 0.91 | 84 | empty |
| 4 | 383 | 0.83 | 0.92 | 53 | empty |
| 5 | 507 | 0.81 | 0.88 | 71 | empty |
Interfaces
3 interfaces between chains.
- C–B · 5652 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 5615 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 5613 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 36 disulfide (N-glycosylation, 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 P0DTC2
- Elsewhere: RCSB PDB 9CRH · PDBe 9CRH · UniProt P0DTC2
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