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Crystal structure of the homotrimer of fusion glycoprotein E1 from semliki forest virus.
Analyse Crystal structure of the homotrimer of fusion glycoprotein E1 from semliki… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RER
- Type
- protein
- Length
- 1,173 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural polyprotein
- UniProt
- P03315
- Ligands
- NAG, BMA, MAN, FUL, FUC, HO, BR, PO4
- Pockets
- 15 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Structural polyprotein | protein | 391 | 4% helix, 42% strand | P03315 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FUL · beta-L-fucopyranose · sugar · chains A
- 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 | 847 | 0.90 | 0.94 | 104 | BR, PO4 |
| 2 | 274 | 0.82 | 0.93 | 45 | BR |
| 3 | 64 | 0.74 | 0.99 | 18 | empty |
| 4 | 241 | 0.63 | 0.82 | 39 | empty |
| 5 | 195 | 0.59 | 0.81 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2335 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2331 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2316 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1RER · Crystal structure of the homotrimer of fusion glycoprotein E1 from Semliki Forest Virus. · 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 1RER · PDBe 1RER · UniProt P03315
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