Research workbench
Cryoem structure of the MDA5-dsrna filament in complex with ADP-ALF4
Analyse Cryoem structure of the MDA5-dsrna filament in complex with ADP-ALF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GKH
- Type
- protein + RNA
- Length
- 715 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-induced helicase C domain-containing protein 1; RNA…
- EC
- 3.6.4.13
- UniProt
- Q8R5F7
- Ligands
- ADP, ALF, MG, ZN
- Pockets
- 13 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interferon-induced helicase C domain-containing protein 1 (EC 3.6.4.13) | protein | 685 | 45% helix, 13% strand | Q8R5F7 |
| X | RNA (5'-R(P*GP*UP*CP*AP*AP*GP*CP*CP*GP*AP*GP*GP*AP*GP*A)- 3') | rna | 15 | — | — |
| Y | RNA (5'-R(P*UP*CP*UP*CP*CP*UP*CP*GP*GP*CP*UP*UP*GP*AP*C)- 3') | rna | 15 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.85 | 0.90 | 73 | empty |
| 2 | 601 | 0.75 | 0.82 | 70 | ADP, ALF, MG |
| 3 | 316 | 0.72 | 0.86 | 34 | empty |
| 4 | 123 | 0.63 | 0.87 | 17 | empty |
| 5 | 353 | 0.57 | 0.76 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–Y · 1101 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–X · 1023 Ų buried · 16 hydrogen bonds · protein-nucleic
- X–Y · 717 Ų buried · 70 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GKH · CryoEM structure of the MDA5-dsRNA filament in complex with ADP-AlF4 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8R5F7 · AlphaFold monomer V2.0 prediction for interferon-induced helicase C domain-containing… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8R5F7
- Elsewhere: RCSB PDB 6GKH · PDBe 6GKH · UniProt Q8R5F7
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