Research workbench
High-resolution full-length hammerhead ribozyme
Analyse High-resolution full-length hammerhead ribozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZP8
- Type
- RNA
- Length
- 63 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hammerhead ribozyme, enzyme strand; Hammerhead ribozyme, substrate strand
- Ligands
- NA
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hammerhead ribozyme, enzyme strand | rna | 43 | — | — |
| B | Hammerhead ribozyme, substrate strand | rna | 20 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 16 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.63 | 0.76 | 38 | NA |
| 2 | 117 | 0.35 | 0.74 | 16 | NA |
Interfaces
1 interface between chains.
- A–B · 1250 Ų buried · 92 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3ZP8 · High-resolution full-length 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 3ZP8 · PDBe 3ZP8
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