Research workbench
SARS-cov spike glycoprotein
Analyse SARS-cov spike glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WRG
- Type
- protein
- Length
- 2,208 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P59594
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 24% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 736 | 24% helix, 14% strand | P59594 |
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 | 1005 | 0.88 | 0.89 | 111 | empty |
| 2 | 918 | 0.82 | 0.84 | 94 | empty |
| 3 | 801 | 0.81 | 0.84 | 99 | empty |
| 4 | 1047 | 0.81 | 0.82 | 99 | empty |
| 5 | 622 | 0.81 | 0.85 | 87 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2870 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2777 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2774 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5WRG · SARS-CoV spike glycoprotein · the same entry in another collection · chain C against C, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.23
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.23
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.23
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against E, TM-score 0.23
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 P59594
- Elsewhere: RCSB PDB 5WRG · PDBe 5WRG · UniProt P59594
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