Research workbench
Cryo-EM structure of chikungunya virus nonstructural protein 1 with M7GTP
Analyse Cryo-EM structure of chikungunya virus nonstructural protein 1 with M7GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FGG
- Type
- protein
- Length
- 5,412 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
- SAH, MGP, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 30% helix, 27% 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 | 451 | 30% helix, 27% strand | Q8JUX6 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MGP · 7-methyl-guanosine-5'-triphosphate · 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
- MG · Magnesium 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 | 884 | 0.86 | 0.88 | 140 | empty |
| 2 | 929 | 0.84 | 0.86 | 109 | SAH, MGP, MG |
| 3 | 988 | 0.84 | 0.85 | 111 | SAH, MGP, MG |
| 4 | 327 | 0.84 | 0.93 | 47 | empty |
| 5 | 802 | 0.84 | 0.86 | 95 | SAH, MGP, MG |
Interfaces
24 interfaces between chains.
- H–I · 3596 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 3596 Ų buried · 35 hydrogen bonds · protein-protein
- F–G · 3596 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 3595 Ų buried · 34 hydrogen bonds · protein-protein
- J–K · 3591 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 7FGG · Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GTP · 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 7FGG · PDBe 7FGG · UniProt Q8JUX6
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