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The crystal structure of human ARGONAUTE2 bound to a guide and target RNA containing seed pairing from 2-9
Analyse The crystal structure of human ARGONAUTE2 bound to a guide and target RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W5O
- Type
- protein + RNA
- Length
- 829 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2; RNA (5'- R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*CP*UP*UP…
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Ligands
- IPH, MG, PO4
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 801 | 32% helix, 27% strand | Q9UKV8 |
| B | RNA (5'- R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*CP*UP*UP*U)-3') | rna | 19 | — | — |
| D | RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*AP*A)-3') | rna | 9 | — | — |
Ligands and binding sites
- IPH · Phenol · ligand · 4 copies · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
- PO4 · Phosphate ion · ion · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.87 | 0.89 | 115 | MG |
| 2 | 174 | 0.67 | 0.87 | 20 | empty |
| 3 | 275 | 0.64 | 0.81 | 32 | empty |
| 4 | 85 | 0.53 | 0.85 | 14 | empty |
| 5 | 56 | 0.46 | 0.84 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2422 Ų buried · 69 hydrogen bonds · protein-nucleic
- A–D · 933 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–D · 411 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 4W5O · The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed… · 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 0.98
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 4W5O · PDBe 4W5O · UniProt Q9UKV8
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