Research workbench
Cryoem structure of disease related M854K MDA5-dsrna filament in complex with ADP-ALF4(MAJOR class)
Analyse Cryoem structure of disease related M854K MDA5-dsrna filament in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NIQ
- Type
- protein + RNA
- Length
- 701 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, ZN
- Pockets
- 11 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Interferon-induced helicase C domain-containing protein 1 (EC 3.6.4.13) | protein | 673 | 48% helix, 14% strand | Q8R5F7 |
| C | RNA (5'-R(P*CP*AP*AP*GP*CP*CP*GP*AP*GP*GP*AP*GP*AP*U)-3') | rna | 14 | — | — |
| G | RNA (5'-R(P*AP*UP*CP*UP*CP*CP*UP*CP*GP*GP*CP*UP*UP*G)-3') | rna | 14 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- ALF · Tetrafluoroaluminate ion · ligand · chains B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.85 | 0.88 | 79 | empty |
| 2 | 774 | 0.78 | 0.82 | 67 | ADP, ALF |
| 3 | 537 | 0.75 | 0.83 | 44 | empty |
| 4 | 296 | 0.72 | 0.85 | 45 | empty |
| 5 | 186 | 0.50 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1004 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–G · 970 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–G · 666 Ų buried · 74 hydrogen bonds · nucleic-nucleic
Compared structures
- 7NIQ · CryoEM structure of disease related M854K MDA5-dsRNA filament in complex with… · the same entry in another collection · chain B against B, 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 B 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 7NIQ · PDBe 7NIQ · UniProt Q8R5F7
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