Research workbench
Crystal structure of the hairpin ribozyme with a 2'OME substrate and N1-deazaadenosine at position A10
Analyse Crystal structure of the hairpin ribozyme with a 2'OME substrate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I2S
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'; DNA/RNA (30-mer)…
- Ligands
- NCO, S9L, SO4
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*GP*U)-3' | rna | 13 | — | — |
| B | DNA/RNA (30-mer) | rna | 29 | — | — |
| C | 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP *C)-3' | rna | 19 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains B, C, A
- S9L · 2-[2-(2-hydroxyethoxy)ethoxy]ethyl dihydrogen phosphate · ligand · chains B, C
- SO4 · Sulfate ion · ion · chains A, B
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 | 218 | 0.44 | 0.74 | 17 | NCO |
| 2 | 179 | 0.42 | 0.74 | 18 | empty |
| 3 | 146 | 0.37 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1018 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–B · 806 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–C · 345 Ų buried · 10 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 3I2S · Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at… · 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 3I2S · PDBe 3I2S
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