Research workbench
SARS spike glycoprotein, stabilized variant, two S1 ctds in the upwards conformation
Analyse SARS spike glycoprotein, stabilized variant, two S1 ctds in the upwards… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CRX
- Type
- protein
- Length
- 3,203 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN
- UniProt
- P59594, D9IEJ2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 1068 | 20% helix, 35% strand | P59594, D9IEJ2 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 1069 | 20% helix, 35% strand | P59594, D9IEJ2 |
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 1066 | 20% helix, 33% strand | P59594, D9IEJ2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 61 copies · chains B, C, A
- BMA · beta-D-mannopyranose · sugar · 8 copies
- MAN · alpha-D-mannopyranose · sugar · 5 copies
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 | 731 | 0.87 | 0.90 | 87 | empty |
| 2 | 819 | 0.84 | 0.86 | 88 | empty |
| 3 | 339 | 0.75 | 0.87 | 52 | empty |
| 4 | 289 | 0.75 | 0.88 | 43 | empty |
| 5 | 824 | 0.75 | 0.79 | 78 | empty |
Interfaces
3 interfaces between chains.
- C–A · 5210 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 4356 Ų buried · 38 hydrogen bonds · protein-protein
- B–A · 4313 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 34 glycan (disulfide, N-glycosylation).
Compared structures
- 6CRX · SARS Spike Glycoprotein, Stabilized variant, two S1 CTDs in the upwards conformation · the same entry in another collection · chain A against A, 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 0.16
- 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 0.16
- 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 0.16
- 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 0.16
- 3SCK · 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 0.16
- 3SCK · 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 0.16
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
- Every structure of UniProt D9IEJ2
- Elsewhere: RCSB PDB 6CRX · PDBe 6CRX · UniProt P59594 · UniProt D9IEJ2
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