Research workbench
Cryo-EM structure of chikungunya virus nonstructural protein 1 with M7GPPP-au
Analyse Cryo-EM structure of chikungunya virus nonstructural protein 1 with M7GPPP-au in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FGI
- Type
- protein
- Length
- 5,244 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, GTA, U, G, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 31% helix, 28% 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 | 437 | 31% helix, 28% 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
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- U · Uridine-5'-monophosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- G · Guanosine-5'-monophosphate · 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 | 372 | 0.84 | 0.93 | 49 | empty |
| 2 | 380 | 0.84 | 0.93 | 50 | empty |
| 3 | 386 | 0.84 | 0.92 | 49 | empty |
| 4 | 386 | 0.84 | 0.92 | 51 | empty |
| 5 | 368 | 0.84 | 0.93 | 47 | empty |
Interfaces
24 interfaces between chains.
- C–D · 3101 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 3091 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 3090 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 3090 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 3089 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7FGI · Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7Gppp-AU · 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 7FGI · PDBe 7FGI · UniProt Q8JUX6
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