MolNFT v1 · #119756 · protein + DNA
Structure of the argonaute protein from methanocaldcoccus janaschii in complex with guide DNA
5G5T: “Structure of the argonaute protein from methanocaldcoccus janaschii in complex with guide DNA”. X-ray diffraction, 2 ligands (MG, SO4), 9 pockets (best druggability 0.62). MolNFT v1 #119756 on GenesisL1: 3D structure, binding sites…
- PDB
- 5G5T
- Type
- protein + DNA
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute; Guide DNA
- UniProt
- Q58717
- Ligands
- MG, SO4
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 670 | 30% helix, 30% strand | Q58717 |
| D | Guide DNA | dna | 8 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.62 | 0.81 | 35 | SO4 |
| 2 | 505 | 0.61 | 0.75 | 56 | empty |
| 3 | 310 | 0.60 | 0.78 | 26 | empty |
| 4 | 111 | 0.51 | 0.81 | 18 | empty |
| 5 | 64 | 0.45 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 1192 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 5G5T · Structure of the Argonaute protein from Methanocaldcoccus janaschii in complex with guide… · 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 0.91
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 Q58717
- Elsewhere: RCSB PDB 5G5T · PDBe 5G5T · UniProt Q58717
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.