Research workbench
Structure of the tetrahymena ribozyme: base triple sandwich and metal ion at the active site
Analyse Structure of the tetrahymena ribozyme: base triple sandwich and metal ion at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X8W
- Type
- RNA
- Length
- 968 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahymena ribozyme RNA
- Ligands
- MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tetrahymena ribozyme RNA | rna | 242 | — | — |
| B | Tetrahymena ribozyme RNA | rna | 247 | — | — |
| C | Tetrahymena ribozyme RNA | rna | 237 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 38 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.82 | 0.85 | 57 | empty |
| 2 | 847 | 0.81 | 0.84 | 56 | MG |
| 3 | 768 | 0.80 | 0.84 | 46 | empty |
| 4 | 1058 | 0.70 | 0.75 | 61 | MG |
| 5 | 1073 | 0.69 | 0.75 | 61 | MG |
Interfaces
3 interfaces between chains.
- B–C · 1030 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–D · 1010 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- A–B · 211 Ų buried · 8 hydrogen bonds · nucleic-nucleic
Compared structures
- 1X8W · Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active… · 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 1X8W · PDBe 1X8W
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.