MolNFT v1 · #166090 · RNA
Pistol ribozyme product crystal soaked in MN2+
6UFK · RNA (50-mer): “Pistol ribozyme product crystal soaked in MN2+”. X-ray diffraction, 1 ligand (MN), 6 pockets (best druggability 0.74). MolNFT v1 #166090 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UFK
- 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
- MN
- Pockets
- 6 · best druggability 0.74
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
- MN · Manganese (II) ion · metal · 22 copies · chains A, B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.74 | 0.83 | 35 | MN |
| 2 | 235 | 0.67 | 0.85 | 21 | MN |
| 3 | 276 | 0.48 | 0.74 | 18 | MN |
| 4 | 227 | 0.42 | 0.73 | 17 | MN |
| 5 | 89 | 0.38 | 0.78 | 14 | MN |
Interfaces
7 interfaces between chains.
- C–D · 569 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–B · 547 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- A–E · 365 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- C–F · 361 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- A–C · 304 Ų buried · 11 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6UFK · Pistol ribozyme product crystal soaked in Mn2+ · 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 6UFK · PDBe 6UFK
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.