MolNFT v1 · #116850 · RNA
Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-wt ribozyme in MG2+
5DQK · RNA (48-mer): “Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-wt…”. X-ray diffraction, 2 ligands (K, MG), 2 pockets (best druggability 0.58). MolNFT v1 #116850 on…
- PDB
- 5DQK
- Type
- RNA
- Length
- 68 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (48-mer); RNA (5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)…
- Ligands
- K, MG
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (48-mer) | rna | 48 | — | — |
| B | RNA (5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)- R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3') | rna | 20 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.58 | 0.74 | 34 | K |
| 2 | 93 | 0.30 | 0.73 | 12 | MG |
Interfaces
1 interface between chains.
- A–B · 925 Ų buried · 82 hydrogen bonds · nucleic-nucleic
Compared structures
- 5DQK · Two divalent metal ions and conformational changes play roles in the 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 5DQK · PDBe 5DQK
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