MolNFT v1 · #92211 · protein

Crystal structure of arabidopsis thaliana AGO5 mid domain

4G0O · Protein argonaute 5: “Crystal structure of arabidopsis thaliana AGO5 mid domain”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.51). MolNFT v1 #92211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4G0O
Type: protein
Length: 277 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein argonaute 5
UniProt: Q9SJK3
Ligands: SO4
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein argonaute 5	protein	139	45% helix, 21% strand	Q9SJK3
B	Protein argonaute 5	protein	138	43% helix, 21% strand	Q9SJK3

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	211	0.51	0.76	30	empty
2	70	0.38	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 393 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4G0O · Crystal structure of Arabidopsis thaliana AGO5 MID domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9SJK3 · AlphaFold monomer V2.0 prediction for protein argonaute 5 (Q9SJK3) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q9SJK3
Elsewhere: RCSB PDB 4G0O · PDBe 4G0O · UniProt Q9SJK3

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