MolNFT v1 · #117285 · protein + RNA
Structural basis for RNA recognition and activation of rig-I
5E3H · Probable ATP-dependent RNA helicase DDX58: “Structural basis for RNA recognition and activation of rig-I”. X-ray diffraction, 4 ligands (ADP, BEF, MG), 10 pockets (best druggability 0.79). MolNFT v1 #117285 on GenesisL1: 3D…
- PDB
- 5E3H
- Type
- protein + RNA
- Length
- 666 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX58; RNA…
- EC
- 3.6.4.13
- UniProt
- O95786
- Ligands
- ADP, BEF, MG, ZN
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 642 | 46% helix, 16% strand | O95786 |
| B | RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3') | rna | 12 | — | — |
| C | RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3') | rna | 12 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, C
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.79 | 0.82 | 101 | MG |
| 2 | 1029 | 0.75 | 0.78 | 77 | empty |
| 3 | 52 | 0.65 | 0.95 | 19 | empty |
| 4 | 241 | 0.65 | 0.83 | 39 | MG, ADP, BEF |
| 5 | 270 | 0.59 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 932 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 825 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 589 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Compared structures
- 5E3H · Structural Basis for RNA Recognition and Activation of RIG-I · the same entry in another collection · chain A against A, TM-score 1.00
- O95786 · AlphaFold monomer V2.0 prediction for antiviral innate immune response receptor rig-I… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O95786
- Elsewhere: RCSB PDB 5E3H · PDBe 5E3H · UniProt O95786
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