MolNFT v1 · #156800 · protein + RNA
Human ARGONAUTE2-mir-122 bound to a target RNA with three central mismatches (BU3)
6MFR · Protein argonaute-2: “Human ARGONAUTE2-mir-122 bound to a target RNA with three central mismatches (BU3)”. X-ray diffraction, 2 ligands (IPH, PO4), 20 pockets (best druggability 0.86). MolNFT v1 #156800 on GenesisL1: 3D structure…
- PDB
- 6MFR
- Type
- protein + RNA
- Length
- 1,666 residues
- Chains
- 6
- 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
- Ligands
- IPH, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 802 | 30% helix, 26% strand | Q9UKV8 |
| B | Protein argonaute-2 (EC 3.1.26.-) | protein | 795 | 30% 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*U)-3') | rna | 20 | — | — |
| D | RNA (5'- R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*U)-3') | rna | 14 | — | — |
| E | RNA (5'- R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP *a)-3') | rna | 21 | — | — |
| F | RNA (5'- R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP *a)-3') | rna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.86 | 0.88 | 81 | empty |
| 2 | 729 | 0.82 | 0.86 | 41 | empty |
| 3 | 611 | 0.72 | 0.80 | 48 | IPH |
| 4 | 215 | 0.66 | 0.84 | 39 | empty |
| 5 | 168 | 0.66 | 0.87 | 22 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1579 Ų buried · 43 hydrogen bonds · protein-nucleic
- B–D · 1370 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–E · 937 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–F · 899 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–E · 825 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Compared structures
- 6MFR · Human Argonaute2-miR-122 bound to a target RNA with three central mismatches (bu3) · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UKV8 · AlphaFold monomer V2.0 prediction for protein argonaute-2 (Q9UKV8) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 6MFR · PDBe 6MFR · UniProt Q9UKV8
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