Research workbench
Triple mutant (K417N-E484K-N501Y) SARS-cov-2 spike protein in the 3- rbd-up conformation (S-gsas-D614G-K417N-E484K-N501Y)
Analyse Triple mutant (K417N-E484K-N501Y) SARS-cov-2 spike protein in the 3- rbd-up… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CSA
- Type
- protein
- Length
- 3,003 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1001 | 24% helix, 33% strand | P0DTC2 |
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 | 1062 | 0.83 | 0.84 | 113 | empty |
| 2 | 633 | 0.82 | 0.87 | 65 | empty |
| 3 | 204 | 0.81 | 0.95 | 34 | empty |
| 4 | 1094 | 0.81 | 0.82 | 122 | empty |
| 5 | 450 | 0.80 | 0.88 | 56 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5120 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 5078 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 4828 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
- 8CSA · Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 3-RBD-Down 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 8CSA · PDBe 8CSA · UniProt P0DTC2
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