Research workbench
Cryo-EM structure of MDA5-dsrna filament in complex with TRIM65 pspry domain (trimer)
Analyse Cryo-EM structure of MDA5-dsrna filament in complex with TRIM65 pspry domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JL2
- Type
- protein + RNA
- Length
- 2,614 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (44-mer); Interferon-induced helicase C domain-containing protein 1; Tripartite…
- EC
- 3.6.4.13
- UniProt
- Q9BYX4, Q6PJ69
- Ligands
- ADP, ALF, ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | RNA (44-mer) | rna | 44 | — | — |
| Y | RNA (44-mer) | rna | 44 | — | — |
| A, C, E | Interferon-induced helicase C domain-containing protein 1 (EC 3.6.4.13) | protein | 662 | 48% helix, 15% strand | Q9BYX4 |
| B, D, F | Tripartite motif-containing protein 65 | protein | 180 | 3% helix, 41% strand | Q6PJ69 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, C, E
- ALF · Tetrafluoroaluminate ion · ligand · 3 copies · chains A, C, E
- ZN · Zinc ion · metal · 3 copies · chains A, C, E
- MG · Magnesium ion · metal · 3 copies · chains A, C, E
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 | 597 | 0.83 | 0.89 | 64 | empty |
| 2 | 1091 | 0.80 | 0.82 | 94 | empty |
| 3 | 598 | 0.79 | 0.85 | 65 | empty |
| 4 | 573 | 0.75 | 0.82 | 71 | ADP, ALF, MG |
| 5 | 569 | 0.75 | 0.82 | 64 | ADP, ALF, MG |
Interfaces
12 interfaces between chains.
- X–Y · 1903 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- Y–A · 1063 Ų buried · 7 hydrogen bonds · protein-nucleic
- Y–E · 1035 Ų buried · 10 hydrogen bonds · protein-nucleic
- X–A · 970 Ų buried · 12 hydrogen bonds · protein-nucleic
- Y–C · 959 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 7JL2 · Cryo-EM structure of MDA5-dsRNA filament in complex with TRIM65 PSpry domain (Trimer) · the same entry in another collection · chain F against F, TM-score 1.00
- Q6PJ69 · AlphaFold monomer V2.0 prediction for tripartite motif-containing protein 65 (Q6PJ69) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q9BYX4 · 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 Q9BYX4
- Every structure of UniProt Q6PJ69
- Elsewhere: RCSB PDB 7JL2 · PDBe 7JL2 · UniProt Q9BYX4 · UniProt Q6PJ69
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