Research workbench
Alpha variant SARS-cov-2 spike with 1 erect rbd
Analyse Alpha variant SARS-cov-2 spike with 1 erect rbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R14
- Type
- protein
- Length
- 2,939 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 20% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 970 | 21% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 994 | 20% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 975 | 19% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.85 | 0.86 | 135 | empty |
| 2 | 1121 | 0.83 | 0.84 | 115 | empty |
| 3 | 223 | 0.81 | 0.94 | 41 | empty |
| 4 | 1057 | 0.80 | 0.82 | 92 | empty |
| 5 | 1071 | 0.79 | 0.81 | 86 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4746 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4670 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4578 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 glycan, 37 disulfide (N-glycosylation, disulfide).
Compared structures
- 7R14 · Alpha Variant SARS-CoV-2 Spike with 1 Erect RBD · 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 7R14 · PDBe 7R14 · UniProt P0DTC2
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