Research workbench
SARS-cov-2 omicron 1-rbd up spike protein trimer without the P986-P987 stabilizing mutations (S-gsas-omicron)
Analyse SARS-cov-2 omicron 1-rbd up spike protein trimer without the P986-P987… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TL9
- Type
- protein
- Length
- 3,083 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 0.84
Structure
electron microscopy · 3 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1050 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1028 | 22% helix, 29% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1005 | 21% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
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 | 576 | 0.84 | 0.90 | 76 | empty |
| 2 | 1093 | 0.83 | 0.84 | 106 | empty |
| 3 | 503 | 0.83 | 0.89 | 56 | empty |
| 4 | 1061 | 0.81 | 0.83 | 116 | empty |
| 5 | 423 | 0.81 | 0.89 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6125 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 6065 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 4155 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 38 glycan (disulfide, N-glycosylation).
Compared structures
- 7TL9 · SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing… · 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 7TL9 · PDBe 7TL9 · UniProt P0DTC2
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