Research workbench
Cryoem structure of the chikungunya virus NSP1 complex
Analyse Cryoem structure of the chikungunya virus NSP1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z0V
- Type
- protein
- Length
- 5,424 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein P1234
- EC
- 2.1.1.-, 2.7.7.-, 3.1.3.33, 3.4.22.-, 3.6.1.15, 3.6.4.13, 3.1.3.84, 2.7.7.19, 2.7.7.48
- UniProt
- Q8JUX6
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, V, X | Polyprotein P1234 (EC 2.1.1.-, 2.7.7.-, 3.1.3.33, 3.4.22.-, 3.6.1.15, 3.6.4.13, 3.1.3.84, 2.7.7.19, 2.7.7.48) | protein | 452 | 30% helix, 28% strand | Q8JUX6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, C, E, G, I, K, M, O, Q, S, V, X
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 | 1134 | 0.86 | 0.87 | 153 | empty |
| 2 | 960 | 0.84 | 0.86 | 141 | empty |
| 3 | 1017 | 0.83 | 0.84 | 128 | empty |
| 4 | 991 | 0.83 | 0.84 | 125 | empty |
| 5 | 206 | 0.82 | 0.96 | 35 | empty |
Interfaces
24 interfaces between chains.
- M–O · 3419 Ų buried · 40 hydrogen bonds · protein-protein
- O–Q · 3419 Ų buried · 43 hydrogen bonds · protein-protein
- A–X · 3417 Ų buried · 42 hydrogen bonds · protein-protein
- V–X · 3416 Ų buried · 43 hydrogen bonds · protein-protein
- S–V · 3415 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6Z0V · CryoEM structure of the Chikungunya virus nsP1 complex · 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 Q8JUX6
- Elsewhere: RCSB PDB 6Z0V · PDBe 6Z0V · UniProt Q8JUX6
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