Research workbench
Crystal structure of the regulatory domain of human rig-I with bound zn
Analyse Crystal structure of the regulatory domain of human rig-I with bound zn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QFB
- Type
- protein
- Length
- 1,210 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX58
- EC
- 3.6.1.-
- UniProt
- O95786
- Ligands
- ZN
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.1.-) | protein | 121 | 12% helix, 42% strand | O95786 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.82 | 0.84 | 73 | empty |
| 2 | 671 | 0.70 | 0.77 | 46 | empty |
| 3 | 763 | 0.69 | 0.76 | 71 | empty |
| 4 | 322 | 0.59 | 0.77 | 25 | empty |
| 5 | 272 | 0.55 | 0.76 | 33 | empty |
Interfaces
11 interfaces between chains.
- C–E · 538 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 457 Ų buried · 7 hydrogen bonds · protein-protein
- G–J · 349 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 332 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 325 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2QFB · Crystal structure of the regulatory domain of human RIG-I with bound Zn · the same entry in another collection · chain J against J, 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 G against A, TM-score 0.97
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 2QFB · PDBe 2QFB · UniProt O95786
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.