MolNFT v1 · #117527 · RNA
Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-MN2+
5EAQ · RNA (48-mer): “Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state…”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.52). MolNFT v1 #117527 on GenesisL1: 3D…
- PDB
- 5EAQ
- 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*(CVC)…
- Ligands
- MN
- Pockets
- 4 · best druggability 0.52
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*(CVC) *UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3') | rna | 20 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.52 | 0.75 | 21 | MN |
| 2 | 114 | 0.33 | 0.73 | 12 | empty |
| 3 | 94 | 0.30 | 0.73 | 14 | MN |
| 4 | 51 | 0.24 | 0.73 | 6 | empty |
Interfaces
1 interface between chains.
- A–B · 952 Ų buried · 61 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5EAQ · Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to… · 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 5EAQ · PDBe 5EAQ
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