Research workbench
Crystal structure of T. thermophilus argonaute E546 mutant protein complexed with DNA guide strand and 15-nt RNA target strand
Analyse Crystal structure of T. thermophilus argonaute E546 mutant protein complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HJF
- Type
- protein + DNA + RNA
- Length
- 695 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute; 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T P*AP*GP*T)-3'…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 665 | 27% helix, 27% strand | Q746M7 |
| X | 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T P*AP*GP*T)-3' | dna | 16 | — | — |
| Y | 5'-R(*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' | rna | 14 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.79 | 0.83 | 54 | empty |
| 2 | 613 | 0.70 | 0.79 | 73 | empty |
| 3 | 74 | 0.64 | 0.93 | 17 | empty |
| 4 | 185 | 0.61 | 0.83 | 32 | empty |
| 5 | 349 | 0.59 | 0.77 | 49 | empty |
Interfaces
3 interfaces between chains.
- A–X · 1396 Ų buried · 33 hydrogen bonds · protein-nucleic
- X–Y · 653 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–Y · 621 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3HJF · Crystal structure of T. thermophilus Argonaute E546 mutant protein complexed with DNA… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q746M7
- Elsewhere: RCSB PDB 3HJF · PDBe 3HJF · UniProt Q746M7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.