MolNFT v1 · #111901 · protein + RNA

Human ARGONAUTE2 bound to T1-dap target RNA

4Z4F · Protein argonaute-2: “Human ARGONAUTE2 bound to T1-dap target RNA”. X-ray diffraction, 2 ligands (IPH, MG), 8 pockets (best druggability 0.88). MolNFT v1 #111901 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Z4F
Type: protein + RNA
Length: 828 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*UP*U)-3'…
EC: 3.1.26.-
UniProt: Q9UKV8
Ligands: IPH, MG
Pockets: 8 · best druggability 0.88

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	801	31% helix, 26% strand	Q9UKV8
B	RNA (5'- R(PUPUPCPAPCPAPUPUPGPCPCPCPAPAPGPUPUPU)-3')	rna	18	—	—
D	RNA (5'-R(CPAPAPUPGPUPGPAP(N6G)PA)-3')	rna	9	—	—

Ligands and binding sites

IPH · Phenol · ligand · 3 copies · chains A
MG · Magnesium ion · metal · 3 copies · chains A, B, D

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	980	0.88	0.90	104	MG
2	62	0.58	0.90	18	empty
3	100	0.57	0.86	17	empty
4	185	0.56	0.80	23	empty
5	70	0.46	0.82	16	empty

Interfaces

3 interfaces between chains.

A–B · 2201 Å² buried · 63 hydrogen bonds · protein-nucleic
A–D · 897 Å² buried · 8 hydrogen bonds · protein-nucleic
B–D · 406 Å² buried · 29 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

4Z4F · Human Argonaute2 Bound to t1-DAP 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 4Z4F · PDBe 4Z4F · UniProt Q9UKV8

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