Research workbench
Human argonaute-2 bound to a guide RNA with a nucleobase modification at position 1
Analyse Human argonaute-2 bound to a guide RNA with a nucleobase modification at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KI6
- Type
- protein + RNA
- Length
- 808 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2; Mir-122
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Ligands
- IPH
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 798 | 32% helix, 28% strand | Q9UKV8 |
| B | Mir-122 | rna | 10 | — | — |
Ligands and binding sites
- IPH · Phenol · ligand · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.80 | 0.82 | 94 | empty |
| 2 | 75 | 0.47 | 0.82 | 27 | empty |
| 3 | 124 | 0.45 | 0.77 | 23 | empty |
| 4 | 82 | 0.44 | 0.81 | 22 | empty |
| 5 | 88 | 0.37 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1720 Ų buried · 47 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5KI6 · Human Argonaute-2 bound to a guide RNA with a nucleobase modification at position 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKV8 · AlphaFold monomer V2.0 prediction for protein argonaute-2 (Q9UKV8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9UKV8
- Elsewhere: RCSB PDB 5KI6 · PDBe 5KI6 · UniProt Q9UKV8
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