GL1X · GenesisL1 explorer

Research workbench

Human ARGONAUTE3 bound to guide RNA

Analyse Human ARGONAUTE3 bound to guide RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5VM9
Type
protein + RNA
Length
1,590 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Protein argonaute-3; RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3'); RNA…
UniProt
Q9H9G7
Pockets
17 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AProtein argonaute-3protein77929% helix, 25% strandQ9H9G7
BRNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3')rna12——
CProtein argonaute-3protein78529% helix, 26% strandQ9H9G7
DRNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)- 3')rna14——

Pockets

17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110670.760.7987empty
27300.730.7952empty
3500.710.9821empty
47090.700.7754empty
53660.660.8043empty

Interfaces

3 interfaces between chains.

  • C–D · 2031 Ų buried · 44 hydrogen bonds · protein-nucleic
  • A–B · 1890 Ų buried · 53 hydrogen bonds · protein-nucleic
  • A–C · 1397 Ų buried · 16 hydrogen bonds · protein-protein

Compared structures

  • 5VM9 · Human Argonaute3 bound to guide RNA · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9H9G7 · AlphaFold monomer V2.0 prediction for protein argonaute-3 (Q9H9G7) · a predicted model of the same protein · chain C against A, TM-score 0.98

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.