Research workbench
Cryo-EM structures of sads-cov spike glycoproteins
Analyse Cryo-EM structures of sads-cov spike glycoproteins in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M16
- Type
- protein
- Length
- 2,895 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- A0A2P1G1L3
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 965 | 20% helix, 28% strand | A0A2P1G1L3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains B, C, A
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 833 | 0.88 | 0.91 | 63 | empty |
| 2 | 403 | 0.85 | 0.93 | 60 | empty |
| 3 | 496 | 0.84 | 0.90 | 73 | empty |
| 4 | 448 | 0.84 | 0.91 | 71 | empty |
| 5 | 262 | 0.82 | 0.93 | 47 | empty |
Interfaces
3 interfaces between chains.
- B–A · 5390 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 5385 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 5382 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 6M16 · Cryo-EM structures of SADS-CoV spike glycoproteins · the same entry in another collection · chain B against B, 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 A0A2P1G1L3
- Elsewhere: RCSB PDB 6M16 · PDBe 6M16 · UniProt A0A2P1G1L3
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