Research workbench
Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 1-RBD-up conformation (S-GSAS-D614G-K417N-E484K-N501Y)
Analyse Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 1-RBD-up… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LWW
- Type
- protein
- Length
- 2,982 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.0 · 3 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 995 | 24% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 995 | 24% helix, 33% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 992 | 23% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 50 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.86 | 0.88 | 93 | empty |
| 2 | 624 | 0.86 | 0.90 | 73 | empty |
| 3 | 1111 | 0.79 | 0.80 | 110 | empty |
| 4 | 755 | 0.76 | 0.81 | 92 | empty |
| 5 | 403 | 0.75 | 0.85 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5381 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 5157 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 4418 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 glycan, 37 disulfide (N-glycosylation, disulfide).
Compared structures
- 7LWW · Triple mutant (K417N-E484K-N501Y) SARS-cov-2 spike protein in the 1- rbd-up conformation… · 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 7LWW · PDBe 7LWW · UniProt P0DTC2
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