Research workbench
Human ARGONAUTE2-mir-122 bound to a target RNA with four central mismatches (BU4)
Analyse Human ARGONAUTE2-mir-122 bound to a target RNA with four central mismatches… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NIT
- Type
- protein + RNA
- Length
- 1,658 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
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 798 | 30% helix, 27% strand | Q9UKV8 |
| B | Protein argonaute-2 (EC 3.1.26.-) | protein | 793 | 29% 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*UP*U)- 3') | rna | 17 | — | — |
| D | 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 | 12 | — | — |
| E | RNA (5'- R(P*AP*AP*CP*AP*CP*CP*AP*UP*CP*CP*AP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)- 3') | rna | 19 | — | — |
| F | RNA (5'- R(P*AP*AP*CP*AP*CP*CP*AP*UP*CP*CP*AP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)- 3') | rna | 19 | — | — |
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.84 | 0.86 | 87 | empty |
| 2 | 755 | 0.80 | 0.84 | 43 | empty |
| 3 | 806 | 0.76 | 0.80 | 78 | empty |
| 4 | 341 | 0.73 | 0.85 | 51 | empty |
| 5 | 181 | 0.61 | 0.83 | 21 | empty |
Interfaces
7 interfaces between chains.
- B–D · 1285 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–C · 1248 Ų buried · 37 hydrogen bonds · protein-nucleic
- B–F · 1168 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 810 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–E · 732 Ų buried · 64 hydrogen bonds · nucleic-nucleic
Compared structures
- 6NIT · Human Argonaute2-miR-122 bound to a target RNA with four central mismatches (bu4) · 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 0.92
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 6NIT · PDBe 6NIT · UniProt Q9UKV8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.