Research workbench
An all-RNA hairpin ribozyme with mutation U39C
Analyse An all-RNA hairpin ribozyme with mutation U39C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X9K
- Type
- RNA
- Length
- 62 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3'…
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3' | rna | 13 | — | — |
| B | 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3' | rna | 13 | — | — |
| C | 5'- R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3' | rna | 17 | — | — |
| D | 5'- R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) -3' | rna | 19 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.50 | 0.75 | 17 | empty |
| 2 | 152 | 0.38 | 0.73 | 17 | empty |
| 3 | 78 | 0.27 | 0.72 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 860 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- A–B · 643 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–D · 370 Ų buried · 10 hydrogen bonds · nucleic-nucleic
- B–C · 201 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- B–D · 187 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Compared structures
- 1X9K · An all-RNA Hairpin Ribozyme with mutation U39C · 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 1X9K · PDBe 1X9K
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.