MolNFT v1 · #124918 · RNA
Crystal structure of pistol, a class of self-cleaving ribozyme
5KTJ · Pistol (50-mer): “Crystal structure of pistol, a class of self-cleaving ribozyme”. X-ray diffraction, 3 ligands (NCO, MG, SM), 4 pockets (best druggability 0.78). MolNFT v1 #124918 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KTJ
- Type
- RNA
- Length
- 130 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pistol (50-mer); RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*GP*UP*CP*CP*AP*A)- 3')
- Ligands
- NCO, MG, SM
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pistol (50-mer) | rna | 50 | — | — |
| B, D | RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*GP*UP*CP*CP*AP*A)- 3') | rna | 15 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 10 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 19 copies · chains A, B, C, D
- SM · Samarium (III) ion · metal · 10 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.78 | 0.81 | 63 | MG, NCO |
| 2 | 193 | 0.45 | 0.75 | 18 | MG, NCO |
| 3 | 171 | 0.40 | 0.73 | 16 | SM, MG |
| 4 | 113 | 0.32 | 0.72 | 17 | SM, MG |
Interfaces
3 interfaces between chains.
- C–D · 905 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–B · 896 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–C · 311 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5KTJ · Crystal structure of Pistol, a class of self-cleaving ribozyme · 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 5KTJ · PDBe 5KTJ
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