MolNFT v1 · #119755 · protein
Structure of the argonaute protein from methanocaldcoccus janaschii
5G5S: “Structure of the argonaute protein from methanocaldcoccus janaschii”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.79). MolNFT v1 #119755 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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.
| Volume (ų) | 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
- 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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