Research workbench
Cryoem structure of MDA5-dsrna filament in complex with ADP with 92- degree helical twist
Analyse Cryoem structure of MDA5-dsrna filament in complex with ADP with 92- degree… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BKQ
- Type
- protein + RNA
- Length
- 670 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of interferon-induced helicase C domain- containing protein 1; RNA…
- EC
- 3.6.4.13
- UniProt
- Q8R5F7
- Ligands
- ADP, ZN
- Pockets
- 16 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of interferon-induced helicase C domain- containing protein 1 (EC 3.6.4.13) | protein | 640 | 48% helix, 12% strand | Q8R5F7 |
| X | RNA (5'-R(P*UP*CP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*AP*CP*G)- 3') | rna | 15 | — | — |
| Y | RNA (5'-R(P*CP*GP*UP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*GP*A)- 3') | rna | 15 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.81 | 0.88 | 65 | empty |
| 2 | 134 | 0.73 | 0.92 | 26 | empty |
| 3 | 309 | 0.72 | 0.86 | 32 | empty |
| 4 | 129 | 0.63 | 0.87 | 28 | empty |
| 5 | 98 | 0.62 | 0.87 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–Y · 1053 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–X · 897 Ų buried · 10 hydrogen bonds · protein-nucleic
- X–Y · 746 Ų buried · 89 hydrogen bonds · nucleic-nucleic
Compared structures
- 7BKQ · CryoEM structure of MDA5-dsRNA filament in complex with ADP with 92-degree helical twist · 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 0.97
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 7BKQ · PDBe 7BKQ · UniProt Q8R5F7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.