Research workbench
Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from sfv into subtomogram averaged chikv E1 glycoprotein density
Analyse Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from sfv… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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