Research workbench
The complex structure of CHIKV envelope glycoprotein bound to human MXRA8
Analyse The complex structure of CHIKV envelope glycoprotein bound to human MXRA8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JO8
- Type
- protein
- Length
- 3,019 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.495
- Source
- Chikungunya virus; Homo sapiens
- Molecule
- Togavirin; Chikv E1; Matrix remodeling-associated protein 8
- EC
- 3.4.21.90
- UniProt
- C8YZ73, A4L787, Q9BRK3
- Ligands
- NAG, NDG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 3.495 · 5 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Togavirin (EC 3.4.21.90) | protein | 393 | 9% helix, 45% strand | C8YZ73 |
| B, D, F | Chikv E1 | protein | 393 | 5% helix, 46% strand | A4L787 |
| C | Togavirin (EC 3.4.21.90) | protein | 338 | 1% helix, 49% strand | C8YZ73 |
| E | Togavirin (EC 3.4.21.90) | protein | 335 | 1% helix, 48% strand | C8YZ73 |
| M, N, O | Matrix remodeling-associated protein 8 | protein | 258 | 5% helix, 37% strand | Q9BRK3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, D, F, A, M
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.86 | 0.87 | 99 | empty |
| 2 | 1079 | 0.85 | 0.86 | 80 | empty |
| 3 | 885 | 0.85 | 0.87 | 88 | empty |
| 4 | 1032 | 0.83 | 0.85 | 99 | empty |
| 5 | 845 | 0.83 | 0.86 | 85 | empty |
Interfaces
21 interfaces between chains.
- A–B · 2598 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2499 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2484 Ų buried · 28 hydrogen bonds · protein-protein
- E–M · 1273 Ų buried · 15 hydrogen bonds · protein-protein
- A–O · 1073 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6JO8 · The complex structure of chikv envelope glycoprotein bound to human MXRA8 · the same entry in another collection · chain O against O, TM-score 1.00
- Q9BRK3 · AlphaFold monomer V2.0 prediction for matrix remodeling-associated protein 8 (Q9BRK3) · a predicted model of the same protein · chain M against A, TM-score 0.82
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 C8YZ73
- Every structure of UniProt A4L787
- Every structure of UniProt Q9BRK3
- Elsewhere: RCSB PDB 6JO8 · PDBe 6JO8 · UniProt C8YZ73 · UniProt A4L787 · UniProt Q9BRK3
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