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Human ARGONAUTE2 bound to T1-C target RNA

Analyse Human ARGONAUTE2 bound to T1-C target RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Z4C
Type: protein + RNA
Length: 830 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*U)…
EC: 3.1.26.-
UniProt: Q9UKV8
Ligands: IPH, MG, PO4
Pockets: 6 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein argonaute-2 (EC 3.1.26.-)	protein	803	31% helix, 26% strand	Q9UKV8
B	RNA (5'- R(PUPUPCPAPCPAPUPUPGPCPCPCPAPAPGPUPCPUP*U)-3')	rna	18	—	—
D	RNA (5'-R(CPAPAPUPGPUPGPAP*C)-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 · 2 copies · chains A, B
IPA · Isopropyl alcohol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1164	0.87	0.89	115	MG
2	199	0.70	0.87	30	empty
3	184	0.62	0.83	25	empty
4	223	0.59	0.80	37	empty
5	102	0.44	0.79	23	IPH

Interfaces

3 interfaces between chains.

A–B · 2325 Å² buried · 73 hydrogen bonds · protein-nucleic
A–D · 799 Å² buried · 13 hydrogen bonds · protein-nucleic
B–D · 411 Å² buried · 36 hydrogen bonds · nucleic-nucleic

Compared structures

4Z4C · Human Argonaute2 Bound to t1-C Target RNA · 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 4Z4C · PDBe 4Z4C · UniProt Q9UKV8

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