MolNFT v1 · #57169 · RNA
The structural basis of hammerhead ribozyme self-cleavage
379D · RNA (5'- R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)…: “The structural basis of hammerhead ribozyme self-cleavage”. X-ray diffraction, 1 ligand (CO), 2 pockets (best druggability 0.26). MolNFT v1 #57169 on GenesisL1: 3D…
- PDB
- 379D
- Type
- RNA
- Length
- 41 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'); RNA (5'…
- Ligands
- CO
- Pockets
- 2 · best druggability 0.26
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (5'- R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3') | rna | 16 | — | — |
| B | RNA (5'- R(*GP*GP*CP*CP*GP*AP*AP*AP*CP*UP*CP*GP*UP*AP*AP*GP*A P*GP*UP*CP*AP*CP*CP*AP*C)-3') | rna | 25 | — | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.26 | 0.73 | 11 | empty |
| 2 | 81 | 0.26 | 0.71 | 13 | CO |
Interfaces
1 interface between chains.
- A–B · 1030 Ų buried · 69 hydrogen bonds · nucleic-nucleic
Compared structures
- 379D · The structural basis of hammerhead ribozyme self-cleavage · 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 379D · PDBe 379D
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