MolNFT v1 · #85471 · protein
Crystal structure of the rubella virus envelope glycoprotein E1 in post-fusion form (crystal form I)
4ADI · E1 envelope glycoprotein: “Crystal structure of the rubella virus envelope glycoprotein E1 in post-fusion form (crystal form I)”. X-ray diffraction, 3 ligands (NAG, NGA, NA), 17 pockets (best druggability 0.88). MolNFT v1 #85471 on…
- PDB
- 4ADI
- Type
- protein
- Length
- 1,274 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E1 envelope glycoprotein
- UniProt
- P08563
- Ligands
- NAG, NGA, NA
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E1 envelope glycoprotein | protein | 425 | 10% helix, 44% strand | P08563 |
| B | E1 envelope glycoprotein | protein | 423 | 10% helix, 43% strand | P08563 |
| C | E1 envelope glycoprotein | protein | 426 | 10% helix, 44% strand | P08563 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 6 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 15 copies · chains A, C, B
- ACT · Acetate ion · additive · 7 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.88 | 0.93 | 86 | empty |
| 2 | 166 | 0.75 | 0.92 | 45 | empty |
| 3 | 288 | 0.73 | 0.87 | 49 | GOL |
| 4 | 209 | 0.71 | 0.87 | 42 | GOL |
| 5 | 220 | 0.70 | 0.87 | 50 | GOL, PEG |
Interfaces
3 interfaces between chains.
- A–B · 3079 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 3012 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 3003 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 12 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 4ADI · 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 4ADI · PDBe 4ADI · UniProt P08563
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