MolNFT v1 · #153801 · RNA
The structure of hatchet ribozyme
6JQ5 · RNA (82-mer): “The structure of hatchet ribozyme”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.69). MolNFT v1 #153801 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JQ5
- Type
- RNA
- Length
- 163 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (82-mer)
- Ligands
- MG
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (82-mer) | rna | 82 | — | — |
| B | RNA (82-mer) | rna | 81 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.69 | 0.77 | 61 | empty |
| 2 | 267 | 0.56 | 0.78 | 20 | empty |
| 3 | 246 | 0.54 | 0.78 | 30 | empty |
| 4 | 325 | 0.53 | 0.75 | 21 | empty |
| 5 | 136 | 0.41 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2158 Ų buried · 149 hydrogen bonds · nucleic-nucleic
Compared structures
- 6JQ5 · The structure of Hatchet 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 6JQ5 · PDBe 6JQ5
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