MolNFT v1 · #145569 · protein
SARS spike glycoprotein, stabilized variant, two S1 ctds in the upwards conformation
6CRX · Spike GLYCOPROTEIN,FIBRITIN: “SARS spike glycoprotein, stabilized variant, two S1 ctds in the upwards conformation”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.87). MolNFT v1 #145569 on…
- 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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