MolNFT v1 · #66300 · protein + DNA + RNA
Crystal structure of T. thermophilus argonaute complexed with DNA guide strand and 19-nt RNA target strand
3HM9: “Crystal structure of T. thermophilus argonaute complexed with DNA guide strand and 19-nt RNA target strand”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.81). MolNFT v1 #66300 on GenesisL1: 3D structure, binding…
- PDB
- 3HM9
- Type
- protein + DNA + RNA
- Length
- 683 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
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 654 | 25% helix, 25% 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(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP *G)-3' | rna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.81 | 0.83 | 59 | empty |
| 2 | 569 | 0.67 | 0.77 | 68 | empty |
| 3 | 344 | 0.63 | 0.79 | 34 | empty |
| 4 | 116 | 0.59 | 0.85 | 33 | empty |
| 5 | 66 | 0.44 | 0.83 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–X · 1327 Ų buried · 35 hydrogen bonds · protein-nucleic
- X–Y · 616 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- A–Y · 517 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3HM9 · Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt… · 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 3HM9 · PDBe 3HM9 · UniProt Q746M7
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