Research workbench
Crystal structure of the rubella virus glycoprotein E1 in its post- fusion form crystallized in presence of 20MM of calcium acetate
Analyse Crystal structure of the rubella virus glycoprotein E1 in its post- fusion form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B3V
- Type
- protein
- Length
- 1,290 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, NA
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | E1 envelope glycoprotein | protein | 430 | 10% helix, 45% 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 · 2 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 15 copies · chains A, B, C
- ACT · Acetate ion · additive · 7 copies · chains A, C, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.88 | 0.93 | 96 | empty |
| 2 | 263 | 0.80 | 0.92 | 60 | empty |
| 3 | 130 | 0.67 | 0.89 | 34 | GOL |
| 4 | 100 | 0.64 | 0.89 | 23 | GOL |
| 5 | 101 | 0.63 | 0.89 | 27 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 3211 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 3168 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3144 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 6 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 4B3V · Crystal structure of the Rubella virus glycoprotein E1 in its 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 4B3V · PDBe 4B3V · UniProt P08563
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