Research workbench
Cryo-EM structure of chikungunya virus nonstructural protein 1 with M7GMP
Analyse Cryo-EM structure of chikungunya virus nonstructural protein 1 with M7GMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FGH
- Type
- protein
- Length
- 5,436 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, G7M, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 30% helix, 26% 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 | 453 | 30% helix, 26% 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
- G7M · N7-methyl-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
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 | 1073 | 0.87 | 0.88 | 137 | SAH, G7M |
| 2 | 956 | 0.84 | 0.85 | 121 | SAH, G7M |
| 3 | 342 | 0.84 | 0.93 | 52 | empty |
| 4 | 333 | 0.84 | 0.93 | 47 | empty |
| 5 | 341 | 0.83 | 0.93 | 49 | empty |
Interfaces
24 interfaces between chains.
- C–D · 3586 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 3585 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 3585 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 3583 Ų buried · 39 hydrogen bonds · protein-protein
- K–L · 3582 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 7FGH · Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GMP · the same entry in another collection · chain C against C, 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 7FGH · PDBe 7FGH · UniProt Q8JUX6
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