Research workbench
SARS-cov-2 S/S2M11/S2M28 local refinement
Analyse SARS-cov-2 S/S2M11/S2M28 local refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LY0
- Type
- protein
- Length
- 354 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2M28 Fab light chain variable region; S2M28 Fab heavy chain variable…
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC
- Pockets
- 2 · best druggability 0.40
Structure
electron microscopy · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 131 | 2% helix, 50% strand | P0DTC2 |
| L | S2M28 Fab light chain variable region | protein | 106 | 7% helix, 44% strand | — |
| H | S2M28 Fab heavy chain variable region | protein | 117 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, H
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.40 | 0.78 | 18 | empty |
| 2 | 77 | 0.31 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 833 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 644 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 592 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7LY0 · SARS-CoV-2 S/S2M11/S2M28 Local Refinement · 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 7LY0 · PDBe 7LY0 · UniProt P0DTC2
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