Research workbench
Electron cryo-microscopy of chikungunya vlp
Analyse Electron cryo-microscopy of chikungunya vlp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NK5
- Type
- protein
- Length
- 4,035 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E1 glycoprotein; E2 glycoprotein; Capsid protein
- UniProt
- Q5XXP3
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | E1 glycoprotein | protein | 439 | 9% helix, 39% strand | Q5XXP3 |
| E, F, G, H | E2 glycoprotein | protein | 419 | 11% helix, 34% strand | Q5XXP3 |
| I | Capsid protein | protein | 150 | 7% helix, 42% strand | Q5XXP3 |
| J, K, L | Capsid protein | protein | 151 | 4% helix, 44% strand | Q5XXP3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, E, B, F, C, G, D, H
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 | 1128 | 0.86 | 0.87 | 133 | empty |
| 2 | 1114 | 0.84 | 0.85 | 94 | empty |
| 3 | 844 | 0.83 | 0.85 | 57 | empty |
| 4 | 1123 | 0.81 | 0.82 | 132 | empty |
| 5 | 177 | 0.81 | 0.95 | 38 | empty |
Interfaces
23 interfaces between chains.
- B–F · 3330 Ų buried · 30 hydrogen bonds · protein-protein
- C–G · 3265 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 3243 Ų buried · 25 hydrogen bonds · protein-protein
- D–H · 3168 Ų buried · 37 hydrogen bonds · protein-protein
- G–K · 647 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6NK5 · Electron Cryo-Microscopy Of Chikungunya VLP · 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 Q5XXP3
- Elsewhere: RCSB PDB 6NK5 · PDBe 6NK5 · UniProt Q5XXP3
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