MolNFT v1 · #191342 · protein
Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from sfv into subtomogram averaged chikv E1 glycoprotein density
8D87 · Spike glycoprotein E1: “Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from sfv into subtomogram averaged chikv…”. Electron microscopy, 9 ligands (NAG, BMA, MAN), 15 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 8D87
- Type
- protein
- Length
- 1,173 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein E1
- UniProt
- P03315
- Ligands
- NAG, BMA, MAN, FUL, NDG, FUC, HO, BR, PO4
- Pockets
- 15 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 4% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein E1 | protein | 391 | 4% helix, 42% strand | P03315 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FUL · beta-L-fucopyranose · sugar · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B
- HO · Holmium atom · metal · 4 copies · chains A, B, C
- BR · Bromide ion · ion · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.90 | 0.93 | 106 | PO4, BR |
| 2 | 230 | 0.81 | 0.94 | 36 | BR |
| 3 | 64 | 0.73 | 0.99 | 18 | empty |
| 4 | 231 | 0.63 | 0.82 | 40 | empty |
| 5 | 244 | 0.62 | 0.81 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2340 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2324 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2315 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 8D87 · Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from SFV into… · 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 P03315
- Elsewhere: RCSB PDB 8D87 · PDBe 8D87 · UniProt P03315
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.