Research workbench
Characterization of the SARS-cov-2 S protein: biophysical, biochemical, structural, and antigenic analysis
Analyse Characterization of the SARS-cov-2 S protein: biophysical, biochemical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X6P
- Type
- protein
- Length
- 3,051 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1017 | 22% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 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 | 857 | 0.84 | 0.86 | 105 | empty |
| 2 | 1161 | 0.83 | 0.84 | 120 | empty |
| 3 | 1198 | 0.81 | 0.82 | 120 | empty |
| 4 | 521 | 0.81 | 0.87 | 61 | empty |
| 5 | 884 | 0.80 | 0.83 | 112 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4941 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 4920 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4909 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 6X6P · Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and… · 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 6X6P · PDBe 6X6P · UniProt P0DTC2
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