MolNFT v1 · #187389 · protein
One rbd-up 2 of pre-fusion SARS-cov-2 delta variant spike protein
7SBO · Spike glycoprotein: “One rbd-up 2 of pre-fusion SARS-cov-2 delta variant spike protein”. Electron microscopy, 3 ligands (NAG, MAN, FUC), 20 pockets (best druggability 0.85). MolNFT v1 #187389 on GenesisL1: 3D structure, binding…
- PDB
- 7SBO
- Type
- protein
- Length
- 3,267 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1091 | 23% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1082 | 23% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1094 | 24% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 84 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains B
- FUC · alpha-L-fucopyranose · 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 | 767 | 0.85 | 0.88 | 90 | empty |
| 2 | 835 | 0.84 | 0.86 | 113 | empty |
| 3 | 770 | 0.81 | 0.84 | 93 | empty |
| 4 | 412 | 0.80 | 0.89 | 48 | empty |
| 5 | 373 | 0.77 | 0.87 | 33 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5771 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 5700 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 5082 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 41 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SBO · One RBD-up 2 of pre-fusion SARS-CoV-2 Delta variant spike protein · 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 7SBO · PDBe 7SBO · UniProt P0DTC2
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