MolNFT v1 · #156796 · protein + RNA

Human ARGONAUTE2-mir-27A bound to HSUR1 target RNA

6MFN · Protein argonaute-2: “Human ARGONAUTE2-mir-27A bound to HSUR1 target RNA”. X-ray diffraction, 1 ligand (IPH), 8 pockets (best druggability 0.78). MolNFT v1 #156796 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6MFN
Type: protein + RNA
Length: 820 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*GP*UP*G)-3'); RNA…
EC: 3.1.26.-
UniProt: Q9UKV8
Ligands: IPH
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein argonaute-2 (EC 3.1.26.-)	protein	803	32% helix, 27% strand	Q9UKV8
C	RNA (5'-R(PUPUPCPAPCPAPGPUP*G)-3')	rna	8	—	—
E	RNA (5'-R(PUPCPUPGPUPGPAPUPAPA)-3')	rna	9	—	—

Ligands and binding sites

IPH · Phenol · ligand · chains A

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1068	0.78	0.80	63	empty
2	513	0.66	0.78	52	empty
3	173	0.58	0.82	18	empty
4	263	0.57	0.78	33	empty
5	205	0.56	0.79	26	empty

Interfaces

3 interfaces between chains.

A–C · 1110 Å² buried · 36 hydrogen bonds · protein-nucleic
A–E · 438 Å² buried · 6 hydrogen bonds · protein-nucleic
C–E · 325 Å² buried · 26 hydrogen bonds · nucleic-nucleic

Compared structures

6MFN · Human Argonaute2-miR-27a bound to HSUR1 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 0.91

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 6MFN · PDBe 6MFN · UniProt Q9UKV8

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