Research workbench
SARS-cov-2-6P-MUT7 S protein (asymmetric)
Analyse SARS-cov-2-6P-MUT7 S protein (asymmetric) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RU2
- Type
- protein
- Length
- 3,301 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1103 | 23% helix, 32% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 1099 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 62 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 | 880 | 0.88 | 0.90 | 103 | empty |
| 2 | 978 | 0.87 | 0.88 | 126 | empty |
| 3 | 272 | 0.84 | 0.95 | 37 | empty |
| 4 | 452 | 0.84 | 0.91 | 46 | empty |
| 5 | 330 | 0.84 | 0.93 | 41 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6478 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 6476 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 6400 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7RU2 · SARS-CoV-2-6P-Mut7 S protein (asymmetric) · 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 7RU2 · PDBe 7RU2 · UniProt P0DTC2
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