MolNFT v1 · #150300 · protein + RNA
Structure of the rig-I singleton-merten syndrome variant C268F
6GPG · RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3'): “Structure of the rig-I singleton-merten syndrome variant C268F”. X-ray diffraction, 2 ligands (ZN, MG), 12 pockets (best druggability 0.78). MolNFT v1 #150300 on GenesisL1…
- PDB
- 6GPG
- Type
- protein + RNA
- Length
- 677 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3'); Probable ATP-dependent RNA…
- EC
- 3.6.4.13
- UniProt
- O95786
- Ligands
- ZN, MG
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3') | rna | 13 | — | — |
| C | RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3') | rna | 13 | — | — |
| A | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 651 | 46% helix, 16% strand | O95786 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.78 | 0.82 | 68 | empty |
| 2 | 611 | 0.76 | 0.83 | 65 | empty |
| 3 | 299 | 0.72 | 0.85 | 49 | MG |
| 4 | 335 | 0.68 | 0.82 | 48 | empty |
| 5 | 414 | 0.67 | 0.80 | 50 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1020 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–A · 872 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 623 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GPG · Structure of the RIG-I Singleton-Merten syndrome variant C268F · 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 0.93
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 6GPG · PDBe 6GPG · UniProt O95786
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