MolNFT v1 · #91119 · protein + RNA

Human argonaute-2 - mir-20A complex

4F3T · Protein argonaute-2: “Human argonaute-2 - mir-20A complex”. X-ray diffraction, 1 ligand (IPH), 9 pockets (best druggability 0.81). MolNFT v1 #91119 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4F3T
Type: protein + RNA
Length: 815 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein argonaute-2; RNA (5'- R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*G*CP*AP*GP*…
EC: 3.1.26.-
UniProt: Q9UKV8
Ligands: IPH
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein argonaute-2 (EC 3.1.26.-)	protein	801	31% helix, 28% strand	Q9UKV8
R	RNA (5'- R(PUPAPAPAPGPUPGPCPUPUPAPUPAPGPUPGCPAPGPG)-3')	rna	14	—	—

Ligands and binding sites

IPH · Phenol · ligand · 2 copies · chains A

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1130	0.81	0.83	92	empty
2	160	0.54	0.80	28	empty
3	125	0.45	0.77	23	empty
4	165	0.45	0.75	18	empty
5	72	0.45	0.81	18	empty

Interfaces

1 interface between chains.

A–R · 2025 Å² buried · 66 hydrogen bonds · protein-nucleic

Compared structures

4F3T · Human Argonaute-2 - miR-20a complex · 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 0.97

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 4F3T · PDBe 4F3T · UniProt Q9UKV8

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