MolNFT v1 · #156741 · protein + RNA
Human ARGONAUTE2-mir-122 bound to a target RNA with two central mismatches (BU2)
6MDZ · Protein argonaute-2: “Human ARGONAUTE2-mir-122 bound to a target RNA with two central mismatches (BU2)”. X-ray diffraction, 1 ligand (IPH), 20 pockets (best druggability 0.85). MolNFT v1 #156741 on GenesisL1: 3D structure, binding…
- PDB
- 6MDZ
- Type
- protein + RNA
- Length
- 1,671 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
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 804 | 30% helix, 27% strand | Q9UKV8 |
| B | Protein argonaute-2 (EC 3.1.26.-) | protein | 796 | 30% helix, 27% 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*CP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP *a)-3') | rna | 23 | — | — |
| F | RNA (5'- R(P*AP*AP*AP*CP*AP*CP*CP*AP*UP*UP*UP*CP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP *a)-3') | rna | 14 | — | — |
Ligands and binding sites
- IPH · Phenol · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.85 | 0.87 | 78 | empty |
| 2 | 1171 | 0.82 | 0.83 | 60 | empty |
| 3 | 754 | 0.73 | 0.79 | 73 | IPH |
| 4 | 419 | 0.70 | 0.82 | 58 | empty |
| 5 | 145 | 0.66 | 0.88 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1572 Ų buried · 44 hydrogen bonds · protein-nucleic
- B–D · 1324 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–E · 1034 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–F · 851 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–E · 831 Ų buried · 73 hydrogen bonds · nucleic-nucleic
Compared structures
- 6MDZ · Human Argonaute2-miR-122 bound to a target RNA with two central mismatches (bu2) · 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 6MDZ · PDBe 6MDZ · UniProt Q9UKV8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.