MolNFT v1 · #191391 · protein
Cryo-EM structure of SARS-cov-2 beta (B.1.351) spike protein in complex with vh domain F6 (focused refinement of rbd and vh F6)
8DI5 · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 beta (B.1.351) spike protein in complex with vh domain F6 (focused refinement…”. Electron microscopy, 1 ligand (NAG), 2 pockets (best druggability 0.46). MolNFT v1 #191391 on…
- PDB
- 8DI5
- Type
- protein
- Length
- 311 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Vh F6
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.46
Structure
electron microscopy · 2 distinct chains · 12% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 195 | 14% helix, 28% strand | P0DTC2 |
| H | Vh F6 | protein | 116 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
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 | 143 | 0.46 | 0.77 | 21 | empty |
| 2 | 84 | 0.34 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- C–H · 1007 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 8DI5 · Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with VH domain F6… · 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 8DI5 · PDBe 8DI5 · UniProt P0DTC2
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