MolNFT v1 · #66677 · protein + DNA + RNA
Structure of an argonaute complexed with guide DNA and target RNA duplex containing two mismatches.
3HXM: “Structure of an argonaute complexed with guide DNA and target RNA duplex containing two mismatches.”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.74). MolNFT v1 #66677 on GenesisL1: 3D structure, binding sites…
- PDB
- 3HXM
- Type
- protein + DNA + RNA
- Length
- 658 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute; DNA (5'- D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 637 | 30% helix, 28% strand | Q746M7 |
| C | DNA (5'- D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)- 3') | dna | 12 | — | — |
| Y | RNA (5'- R(*UP*AP*UP*AP*CP*AP*AP*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3') | rna | 9 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.74 | 0.78 | 61 | empty |
| 2 | 596 | 0.73 | 0.80 | 66 | empty |
| 3 | 65 | 0.55 | 0.88 | 17 | empty |
| 4 | 50 | 0.51 | 0.87 | 20 | empty |
| 5 | 165 | 0.49 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1300 Ų buried · 37 hydrogen bonds · protein-nucleic
- C–Y · 389 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- A–Y · 385 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 3HXM · Structure of an argonaute complexed with guide DNA and target RNA duplex containing two… · 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 3HXM · PDBe 3HXM · UniProt Q746M7
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