Research workbench
Cryo-EM structure of chikungunya virus nonstructural protein 1 with inhibitor fha
Analyse Cryo-EM structure of chikungunya virus nonstructural protein 1 with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X01
- Type
- protein
- Length
- 5,052 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-capping enzyme NSP1
- EC
- 2.1.1.-, 2.7.7.-
- UniProt
- Q8JUX6
- Ligands
- 7XQ, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | MRNA-capping enzyme NSP1 (EC 2.1.1.-, 2.7.7.-) | protein | 421 | 27% helix, 29% strand | Q8JUX6 |
Ligands and binding sites
- 7XQ · (1R,2S,3S,4R,5R)-3-(6-aminopurin-9-yl)-4-fluoranyl-5-(2-hydroxyethyl)cyclopentane-1,2-diol · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 367 | 0.84 | 0.93 | 47 | empty |
| 2 | 374 | 0.84 | 0.92 | 52 | empty |
| 3 | 374 | 0.84 | 0.92 | 51 | empty |
| 4 | 387 | 0.83 | 0.92 | 53 | empty |
| 5 | 350 | 0.83 | 0.93 | 50 | empty |
Interfaces
24 interfaces between chains.
- A–L · 3123 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3122 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 3120 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 3115 Ų buried · 30 hydrogen bonds · protein-protein
- I–J · 3114 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7X01 · Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with inhibitor FHA · 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 7X01 · PDBe 7X01 · UniProt Q8JUX6
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