Research workbench
Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme
Analyse Structure-based insights into self-cleavage by a four-way junctional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y85
- Type
- RNA
- Length
- 136 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3'); DNA/RNA (50-mer)
- Ligands
- MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA (5'- R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3') | rna | 18 | — | — |
| B, D | DNA/RNA (50-mer) | rna | 50 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 26 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.74 | 0.82 | 42 | MG |
| 2 | 510 | 0.72 | 0.82 | 29 | MG |
| 3 | 296 | 0.63 | 0.81 | 29 | MG |
Interfaces
4 interfaces between chains.
- A–B · 1280 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- C–D · 1273 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- B–D · 322 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–C · 85 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 5Y85 · Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister… · 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 5Y85 · PDBe 5Y85
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