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Structure of the argonaute protein from methanocaldcoccus janaschii

Analyse Structure of the argonaute protein from methanocaldcoccus janaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5G5S
Type: protein
Length: 692 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Argonaute
UniProt: Q58717
Ligands: MG
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Argonaute	protein	692	32% helix, 29% strand	Q58717

Ligands and binding sites

MG · Magnesium ion · metal · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

6 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	872	0.79	0.82	87	empty
2	207	0.53	0.78	34	empty
3	123	0.47	0.78	17	empty
4	173	0.45	0.75	25	empty
5	101	0.37	0.74	15	empty

Compared structures

5G5S · Structure of the Argonaute protein from Methanocaldcoccus janaschii · the same entry in another collection · chain A against A, TM-score 1.00
Q58717 · AlphaFold monomer V2.0 prediction for protein argonaute (Q58717) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 Q58717
Elsewhere: RCSB PDB 5G5S · PDBe 5G5S · UniProt Q58717

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