Research workbench
SARS-cov-2 spike in prefusion state (flexibility analysis, 1-up open conformation)
Analyse SARS-cov-2 spike in prefusion state (flexibility analysis, 1-up open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZP7
- Type
- protein
- Length
- 2,861 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 988 | 22% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 943 | 24% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 930 | 24% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, C, B
- 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 | 868 | 0.86 | 0.88 | 112 | empty |
| 2 | 1178 | 0.82 | 0.83 | 124 | empty |
| 3 | 591 | 0.82 | 0.87 | 52 | empty |
| 4 | 526 | 0.80 | 0.87 | 72 | empty |
| 5 | 782 | 0.80 | 0.83 | 85 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4667 Ų buried · 33 hydrogen bonds · protein-protein
- C–B · 4661 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 4139 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 35 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6ZP7 · SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up open conformation) · 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 6ZP7 · PDBe 6ZP7 · UniProt P0DTC2
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