Research workbench
Crystal structure of the mature envelope glycoprotein complex (spontaneous cleavage) of chikungunya virus.
Analyse Crystal structure of the mature envelope glycoprotein complex (spontaneous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N41
- Type
- protein
- Length
- 775 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, NDG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 envelope glycoprotein | protein | 55 | 38% helix, 16% strand | Q1H8W5 |
| B | E2 envelope glycoprotein | protein | 338 | 3% helix, 51% strand | Q1H8W5 |
| F | E1 envelope glycoprotein | protein | 382 | 5% helix, 49% strand | Q1H8W5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, F
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.81 | 0.82 | 98 | empty |
| 2 | 214 | 0.65 | 0.84 | 44 | empty |
| 3 | 279 | 0.55 | 0.76 | 31 | empty |
| 4 | 98 | 0.51 | 0.82 | 18 | empty |
| 5 | 119 | 0.50 | 0.80 | 24 | empty |
Interfaces
2 interfaces between chains.
- B–F · 2152 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3N41 · Crystal structure of the mature envelope glycoprotein complex (spontaneous cleavage) of… · 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 3N41 · PDBe 3N41 · UniProt Q1H8W5
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