MolNFT v1 · #57092 · RNA
Capturing the structure of a catalytic RNA intermediate: RNA hammerhead ribozyme, MG(II)-soaked
301D: “Capturing the structure of a catalytic RNA intermediate: RNA hammerhead ribozyme, MG(II)-soaked”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.30). MolNFT v1 #57092 on GenesisL1: 3D structure, binding sites and…
- PDB
- 301D
- Type
- RNA
- Length
- 41 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA hammerhead ribozyme
- Ligands
- MG
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA hammerhead ribozyme | rna | 16 | — | — |
| B | RNA hammerhead ribozyme | rna | 25 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.30 | 0.73 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1008 Ų buried · 99 hydrogen bonds · nucleic-nucleic
Compared structures
- 301D · Capturing the structure of a catalytic RNA intermediate: RNA hammerhead 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 301D · PDBe 301D
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