Research workbench
Crystal structure of human rig-I ctd bound to a 14 bp gc 5' ppp dsrna
Analyse Crystal structure of human rig-I ctd bound to a 14 bp gc 5' ppp dsrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LRN
- Type
- protein + RNA
- Length
- 270 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX58; RNA…
- EC
- 3.6.1.-
- UniProt
- O95786
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.1.-) | protein | 121 | 12% helix, 50% strand | O95786 |
| C, D | RNA (5'-R(*(GTP)P*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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.54 | 0.74 | 27 | empty |
| 2 | 199 | 0.42 | 0.73 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 711 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- A–C · 454 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–D · 444 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 166 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–C · 96 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3LRN · Crystal structure of human RIG-I CTD bound to a 14 bp GC 5' ppp 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 0.98
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 3LRN · PDBe 3LRN · UniProt O95786
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.