Research workbench
Cryoem structure of the MDA5-dsrna filament in complex with ATP (10 mm)
Analyse Cryoem structure of the MDA5-dsrna filament in complex with ATP (10 mm) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GKM
- Type
- protein + RNA
- Length
- 717 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
- ATP, ZN
- Pockets
- 10 · best druggability 0.86
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 | 689 | 45% helix, 13% strand | Q8R5F7 |
| X | RNA (5'-R(P*CP*AP*AP*GP*CP*CP*GP*AP*GP*GP*AP*GP*AP*G)-3') | rna | 14 | — | — |
| Y | RNA (5'-R(P*CP*UP*CP*UP*CP*CP*UP*CP*GP*GP*CP*UP*UP*G)-3') | rna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.86 | 0.87 | 108 | empty |
| 2 | 1162 | 0.83 | 0.84 | 81 | empty |
| 3 | 441 | 0.72 | 0.82 | 52 | ATP |
| 4 | 237 | 0.58 | 0.79 | 31 | empty |
| 5 | 92 | 0.44 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–Y · 1205 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–X · 1179 Ų buried · 19 hydrogen bonds · protein-nucleic
- X–Y · 685 Ų buried · 61 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GKM · CryoEM structure of the MDA5-dsRNA filament in complex with ATP (10 mM) · 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 0.99
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 6GKM · PDBe 6GKM · UniProt Q8R5F7
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