Research workbench
Crystal structure of the rubella virus envelope glycoprotein E1 in post-fusion form (crystal form II)
Analyse Crystal structure of the rubella virus envelope glycoprotein E1 in post-fusion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ADG
- Type
- protein
- Length
- 1,294 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E1 envelope glycoprotein
- UniProt
- P08563
- Ligands
- NAG, NGA, CA, CL
- Pockets
- 15 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E1 envelope glycoprotein | protein | 431 | 10% helix, 44% strand | P08563 |
| C | E1 envelope glycoprotein | protein | 432 | 10% helix, 44% strand | P08563 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, B, C
- GOL · Glycerol · additive · 12 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.90 | 0.93 | 137 | empty |
| 2 | 283 | 0.74 | 0.88 | 48 | empty |
| 3 | 195 | 0.70 | 0.88 | 39 | GOL |
| 4 | 136 | 0.64 | 0.87 | 30 | empty |
| 5 | 293 | 0.61 | 0.79 | 48 | GOL, PEG |
Interfaces
3 interfaces between chains.
- B–C · 3171 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3157 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 3139 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 5 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 4ADG · Crystal structure of the Rubella virus envelope Glycoprotein E1 in post-fusion form… · 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 P08563
- Elsewhere: RCSB PDB 4ADG · PDBe 4ADG · UniProt P08563
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