MolNFT v1 · #66360 · protein + DNA + RNA
Crystal structure of T. thermophilus argonaute N546 mutant protein complexed with DNA guide strand and 12-nt RNA target strand
3HO1: “Crystal structure of T. thermophilus argonaute N546 mutant protein complexed with DNA guide strand and 12-nt…”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.80). MolNFT v1 #66360 on GenesisL1: 3D structure…
- PDB
- 3HO1
- Type
- protein + DNA + RNA
- Length
- 698 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 *AP*GP*T)-3'…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 673 | 26% helix, 30% strand | Q746M7 |
| X | 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T *AP*GP*T)-3' | dna | 14 | — | — |
| Y | 5'-R(P*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3' | rna | 11 | — | — |
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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.80 | 0.82 | 72 | empty |
| 2 | 262 | 0.68 | 0.84 | 48 | empty |
| 3 | 149 | 0.48 | 0.78 | 23 | empty |
| 4 | 206 | 0.46 | 0.74 | 31 | empty |
| 5 | 58 | 0.41 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–X · 1620 Ų buried · 46 hydrogen bonds · protein-nucleic
- A–Y · 715 Ų buried · 12 hydrogen bonds · protein-nucleic
- X–Y · 514 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Compared structures
- 3HO1 · Crystal structure of T. thermophilus Argonaute N546 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 3HO1 · PDBe 3HO1 · UniProt Q746M7
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