MolNFT v1 · #108400 · protein + RNA
The crystal structure of human ARGONAUTE2 bound to a guide and target RNA containing seed pairing from 2-8 (long target)
4W5R · Protein argonaute-2: “The crystal structure of human ARGONAUTE2 bound to a guide and target RNA containing seed pairing from 2-8…”. X-ray diffraction, 2 ligands (IPH, MG), 7 pockets (best druggability 0.79). MolNFT v1 #108400 on…
- PDB
- 4W5R
- Type
- protein + RNA
- Length
- 822 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*UP*U)-3'); RNA…
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Ligands
- IPH, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 803 | 31% helix, 27% strand | Q9UKV8 |
| B | RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*UP*U)-3') | rna | 11 | — | — |
| D | RNA (5'-R(P*AP*AP*UP*GP*UP*GP*AP*AP*A)-3') | rna | 8 | — | — |
Ligands and binding sites
- IPH · Phenol · ligand · 3 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B, D
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.79 | 0.82 | 61 | MG |
| 2 | 317 | 0.70 | 0.84 | 43 | empty |
| 3 | 198 | 0.58 | 0.81 | 31 | empty |
| 4 | 139 | 0.54 | 0.82 | 21 | empty |
| 5 | 114 | 0.44 | 0.78 | 26 | IPH |
Interfaces
3 interfaces between chains.
- A–B · 1559 Ų buried · 50 hydrogen bonds · protein-nucleic
- A–D · 775 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 363 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Compared structures
- 4W5R · 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 4W5R · PDBe 4W5R · UniProt Q9UKV8
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