MolNFT v1 · #157601 · protein + RNA
Human ARGONAUTE2-mir-122 bound to a seed and supplementary paired target
6N4O · Protein argonaute-2: “Human ARGONAUTE2-mir-122 bound to a seed and supplementary paired target”. X-ray diffraction, 9 pockets (best druggability 0.78). MolNFT v1 #157601 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N4O
- Type
- protein + RNA
- Length
- 828 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2; RNA (5'- R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP…
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 796 | 29% helix, 26% strand | Q9UKV8 |
| C | RNA (5'- R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)- 3') | rna | 19 | — | — |
| D | RNA (5'- R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3') | rna | 13 | — | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.78 | 0.86 | 44 | empty |
| 2 | 385 | 0.77 | 0.87 | 49 | empty |
| 3 | 363 | 0.76 | 0.87 | 60 | empty |
| 4 | 212 | 0.61 | 0.81 | 36 | empty |
| 5 | 122 | 0.51 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2228 Ų buried · 53 hydrogen bonds · protein-nucleic
- A–D · 934 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 606 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Compared structures
- 6N4O · Human Argonaute2-miR-122 bound to a seed and supplementary paired target · 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 0.93
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 6N4O · PDBe 6N4O · UniProt Q9UKV8
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