Research workbench
SARS-cov-2 spike in prefusion state
Analyse SARS-cov-2 spike in prefusion state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZOW
- Type
- protein
- Length
- 2,862 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 801 | 24% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 943 | 24% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 930 | 24% helix, 29% strand | P0DTC2 |
| a | Spike glycoprotein | protein | 188 | 14% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, C, B, a
- BMA · beta-D-mannopyranose · sugar · 11 copies
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains a
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 | 614 | 0.84 | 0.89 | 78 | empty |
| 2 | 1088 | 0.83 | 0.84 | 113 | empty |
| 3 | 846 | 0.82 | 0.84 | 108 | empty |
| 4 | 1199 | 0.81 | 0.83 | 117 | empty |
| 5 | 422 | 0.78 | 0.87 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4924 Ų buried · 49 hydrogen bonds · protein-protein
- C–B · 4848 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 4282 Ų buried · 41 hydrogen bonds · protein-protein
- A–a · 314 Ų buried · 6 hydrogen bonds · protein-protein
- B–a · 224 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZOW · SARS-CoV-2 spike in prefusion state · the same entry in another collection · chain A against A, TM-score 1.00
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 P0DTC2
- Elsewhere: RCSB PDB 6ZOW · PDBe 6ZOW · UniProt P0DTC2
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