Research workbench
Crystal structure of human rig-I ctd bound to a 14-bp blunt-ended dsrna
Analyse Crystal structure of human rig-I ctd bound to a 14-bp blunt-ended dsrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OG8
- Type
- protein + RNA
- Length
- 282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DDX58; RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
- EC
- 3.6.4.13
- UniProt
- O95786
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 126 | 16% helix, 42% strand | O95786 |
| B | ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 128 | 16% helix, 43% strand | O95786 |
| C, D | RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3') | rna | 14 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.80 | 0.82 | 60 | empty |
| 2 | 62 | 0.40 | 0.80 | 17 | empty |
| 3 | 66 | 0.37 | 0.78 | 17 | empty |
Interfaces
5 interfaces between chains.
- C–D · 699 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- B–D · 384 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–C · 371 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 323 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–C · 276 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 3OG8 · Crystal structure of human RIG-I CTD bound to a 14-bp blunt-ended dsRNA · 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 0.95
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 3OG8 · PDBe 3OG8 · UniProt O95786
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