Research workbench
Pistol ribozyme product crystal structure
Analyse Pistol ribozyme product crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UFJ
- Type
- RNA
- Length
- 130 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (50-mer); RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3'); RNA…
- Ligands
- MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA (50-mer) | rna | 50 | — | — |
| B, D | RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3') | rna | 10 | — | — |
| E, F | RNA (5'-R(*UP*CP*CP*AP*G)-3') | rna | 5 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 17 copies · chains A, B, E, C, D, F
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 | 969 | 0.77 | 0.80 | 63 | MG |
| 2 | 215 | 0.45 | 0.74 | 18 | MG |
| 3 | 218 | 0.43 | 0.73 | 17 | MG |
| 4 | 206 | 0.41 | 0.73 | 18 | MG |
Interfaces
7 interfaces between chains.
- C–D · 572 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–B · 564 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- C–F · 376 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- A–E · 364 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- A–C · 302 Ų buried · 8 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6UFJ · Pistol ribozyme product crystal structure · 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 6UFJ · PDBe 6UFJ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.