MolNFT v1 · #191450 · protein
Cryo-EM structure of spike binding to Fab of neutralizing antibody (locally refined)
8DT3 · Spike glycoprotein: “Cryo-EM structure of spike binding to Fab of neutralizing antibody (locally refined)”. Electron microscopy, 2 ligands (NAG, FUC), 5 pockets (best druggability 0.72). MolNFT v1 #191450 on GenesisL1: 3D structure…
- PDB
- 8DT3
- Type
- protein
- Length
- 485 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain Fab of SW186; Light chain Fab of SW186
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 5 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 253 | 13% helix, 32% strand | P0DTC2 |
| H | Heavy chain Fab of SW186 | protein | 123 | 5% helix, 54% strand | — |
| L | Light chain Fab of SW186 | protein | 109 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, H, L
- FUC · alpha-L-fucopyranose · sugar · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.72 | 0.97 | 22 | empty |
| 2 | 215 | 0.51 | 0.76 | 33 | empty |
| 3 | 138 | 0.48 | 0.78 | 33 | NAG, FUC |
| 4 | 68 | 0.30 | 0.75 | 17 | empty |
| 5 | 56 | 0.26 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 868 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 598 Ų buried · 8 hydrogen bonds · protein-protein
- C–L · 272 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 8DT3 · Cryo-EM structure of spike binding to Fab of neutralizing antibody (locally refined) · the same entry in another collection · chain C against C, 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 8DT3 · PDBe 8DT3 · UniProt P0DTC2
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