Research workbench
SARS spike glycoprotein, trypsin-cleaved, stabilized variant, two S1 ctds in an upwards conformation
Analyse SARS spike glycoprotein, trypsin-cleaved, stabilized variant, two S1 ctds in an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CS1
- Type
- protein
- Length
- 3,202 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 0.88
Structure
electron microscopy · 3 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 1068 | 19% helix, 34% strand | P59594, D9IEJ2 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 1068 | 20% helix, 32% strand | P59594, D9IEJ2 |
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 1066 | 19% helix, 31% strand | P59594, D9IEJ2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains B, A, C
- BMA · beta-D-mannopyranose · sugar · 12 copies
- MAN · alpha-D-mannopyranose · sugar · 9 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 | 874 | 0.88 | 0.91 | 98 | empty |
| 2 | 726 | 0.82 | 0.85 | 74 | empty |
| 3 | 859 | 0.80 | 0.83 | 116 | empty |
| 4 | 547 | 0.78 | 0.85 | 77 | empty |
| 5 | 818 | 0.75 | 0.79 | 85 | empty |
Interfaces
3 interfaces between chains.
- C–A · 5362 Ų buried · 66 hydrogen bonds · protein-protein
- B–A · 4423 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 4371 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 33 glycan (disulfide, N-glycosylation).
Compared structures
- 6CS1 · SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, two S1 CTDs in an upwards… · 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 6CS1 · PDBe 6CS1 · UniProt P59594 · UniProt D9IEJ2
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