Research workbench
South african (B.1.351) SARS-cov-2 spike protein variant (S-gsas- B.1.351) in the 2-rbd-up conformation
Analyse South african (B.1.351) SARS-cov-2 spike protein variant (S-gsas- B.1.351) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LYK
- Type
- protein
- Length
- 2,983 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 0.85
Structure
electron microscopy · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 995 | 23% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 993 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 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 | 951 | 0.85 | 0.87 | 101 | empty |
| 2 | 807 | 0.80 | 0.83 | 75 | empty |
| 3 | 365 | 0.76 | 0.87 | 46 | empty |
| 4 | 335 | 0.74 | 0.86 | 46 | empty |
| 5 | 622 | 0.73 | 0.81 | 49 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5070 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 4603 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4439 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 25 glycan (disulfide, N-glycosylation).
Compared structures
- 7LYK · South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 2-RBD-up… · 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 7LYK · PDBe 7LYK · UniProt P0DTC2
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