Research workbench
Structure of SARS-CoV spike glycoprotein
Analyse Structure of 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
- 5XLR
- Type
- protein
- Length
- 3,066 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Human SARS coronavirus
- Molecule
- Spike glycoprotein
- UniProt
- P59594
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.8 · 1 distinct chain · 20% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1022 | 20% helix, 23% 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 | 1070 | 0.85 | 0.86 | 113 | empty |
| 2 | 777 | 0.81 | 0.84 | 110 | empty |
| 3 | 949 | 0.80 | 0.81 | 115 | empty |
| 4 | 679 | 0.78 | 0.83 | 57 | empty |
| 5 | 476 | 0.77 | 0.85 | 74 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5326 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 5264 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 5236 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 5XLR · Structure of SARS-cov spike glycoprotein · the same entry in another collection · chain A against A, TM-score 1.00
- 3SCJ · 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 0.17
- 3SCJ · 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 0.17
- 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 0.17
- 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 0.17
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 5XLR · PDBe 5XLR · UniProt P59594
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