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Human argonaute-2 paz domain (214-347) in complex with cgugacucu

Analyse Human argonaute-2 paz domain (214-347) in complex with cgugacucu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RA4
Type: protein + RNA
Length: 275 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein argonaute-2; RNA (5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3')
EC: 3.1.26.-
UniProt: Q9UKV8
Pockets: 1 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein argonaute-2 (EC 3.1.26.-)	protein	127	28% helix, 24% strand	Q9UKV8
B	Protein argonaute-2 (EC 3.1.26.-)	protein	130	28% helix, 27% strand	Q9UKV8
L, M	RNA (5'-R(CPGPUPGPAPCPUPCP*U)-3')	rna	9	—	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, L, B, M

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	577	0.76	0.83	49	GOL

Interfaces

5 interfaces between chains.

B–M · 787 Å² buried · 23 hydrogen bonds · protein-nucleic
A–L · 671 Å² buried · 15 hydrogen bonds · protein-nucleic
L–M · 263 Å² buried · 25 hydrogen bonds · nucleic-nucleic
A–M · 168 Å² buried · 3 hydrogen bonds · protein-nucleic
B–L · 118 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6RA4 · Human ARGONAUTE-2 PAZ DOMAIN (214-347) IN COMPLEX WITH CGUGACUCU · 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 6RA4 · PDBe 6RA4 · UniProt Q9UKV8

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