Research workbench
Crystal structure of the mature envelope glycoprotein complex (trypsin cleavage; osmium soak) of chikungunya virus.
Analyse Crystal structure of the mature envelope glycoprotein complex (trypsin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N44
- Type
- protein
- Length
- 783 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 envelope glycoprotein; E2 envelope glycoprotein; E1 envelope glycoprotein
- UniProt
- Q1H8W5
- Ligands
- NAG, OS
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 envelope glycoprotein | protein | 54 | 39% helix, 17% strand | Q1H8W5 |
| B | E2 envelope glycoprotein | protein | 338 | 4% helix, 51% strand | Q1H8W5 |
| F | E1 envelope glycoprotein | protein | 391 | 6% helix, 48% strand | Q1H8W5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, F
- OS · Osmium ion · metal · 6 copies · chains B, F
- ACT · Acetate ion · additive · 3 copies · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.75 | 0.80 | 72 | empty |
| 2 | 486 | 0.73 | 0.82 | 54 | empty |
| 3 | 172 | 0.62 | 0.84 | 42 | empty |
| 4 | 164 | 0.61 | 0.84 | 19 | empty |
| 5 | 339 | 0.55 | 0.74 | 57 | empty |
Interfaces
2 interfaces between chains.
- B–F · 2621 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3N44 · Crystal structure of the mature envelope glycoprotein complex (trypsin cleavage; Osmium… · 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 Q1H8W5
- Elsewhere: RCSB PDB 3N44 · PDBe 3N44 · UniProt Q1H8W5
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