Research workbench
Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 ångströms resolution
Analyse Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OUE
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Substrate strand - minimal junctionless hairpin ribozyme; Loop a ribozyme strand; Loop B…
- Ligands
- NCO, SO4
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Substrate strand - minimal junctionless hairpin ribozyme | rna | 13 | — | — |
| B | Loop a ribozyme strand | rna | 12 | — | — |
| C | Loop B ribozyme strand | rna | 17 | — | — |
| D | Loop B S-turn strand | rna | 19 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.39 | 0.74 | 18 | empty |
| 2 | 158 | 0.38 | 0.73 | 15 | empty |
| 3 | 101 | 0.32 | 0.73 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 888 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- A–B · 676 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–D · 340 Ų buried · 10 hydrogen bonds · nucleic-nucleic
- B–C · 207 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- A–C · 179 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2OUE · Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution · 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 2OUE · PDBe 2OUE
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