Research workbench
Structure of an argonaute complexed with guide DNA and target RNA duplex containing two mismatches.
Analyse Structure of an argonaute complexed with guide DNA and target RNA duplex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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