Research workbench
The structure of native pistol ribozyme, bound to iridium
Analyse The structure of native pistol ribozyme, bound to iridium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K7D
- Type
- RNA
- Length
- 58 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 47-mer; DNA/RNA 11-mer
- Ligands
- IRI, MG
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA 47-mer | rna | 47 | — | — |
| B | DNA/RNA 11-mer | rna | 11 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.68 | 0.79 | 34 | IRI, MG |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Compared structures
- 5K7D · The structure of native pistol ribozyme, bound to Iridium · 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
- Elsewhere: RCSB PDB 5K7D · PDBe 5K7D
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