Research workbench
Mink Variant SARS-CoV-2 Spike in Closed conformation
Analyse Mink Variant SARS-CoV-2 Spike in Closed conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R18
- Type
- protein
- Length
- 3,189 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 3.0 · 1 distinct chain · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1063 | 20% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
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 | 1151 | 0.88 | 0.89 | 117 | empty |
| 2 | 1192 | 0.85 | 0.86 | 144 | empty |
| 3 | 978 | 0.81 | 0.82 | 76 | empty |
| 4 | 1062 | 0.81 | 0.82 | 80 | empty |
| 5 | 910 | 0.81 | 0.83 | 70 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4348 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4348 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 4337 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7R18 · Mink variant SARS-cov-2 spike in closed 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 7R18 · PDBe 7R18 · UniProt P0DTC2
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