MolNFT v1 · #55440 · protein + RNA
Structural insights into RNA recognition by rig-I
2YKG · Probable ATP-dependent RNA helicase DDX58: “Structural insights into RNA recognition by rig-I”. X-ray diffraction, 2 ligands (ZN, SO4), 12 pockets (best druggability 0.72). MolNFT v1 #55440 on GenesisL1: 3D structure, binding sites…
- PDB
- 2YKG
- Type
- protein + RNA
- Length
- 656 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX58; 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'
- EC
- 3.6.4.13
- UniProt
- O95786
- Ligands
- ZN, SO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 636 | 44% helix, 18% strand | O95786 |
| C, D | 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3' | rna | 10 | — | — |
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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.72 | 0.76 | 68 | empty |
| 2 | 488 | 0.66 | 0.77 | 53 | empty |
| 3 | 286 | 0.56 | 0.77 | 38 | empty |
| 4 | 106 | 0.51 | 0.82 | 17 | empty |
| 5 | 91 | 0.44 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 592 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 558 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 505 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2YKG · Structural insights into RNA recognition by 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 0.75
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 2YKG · PDBe 2YKG · UniProt O95786
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