Research workbench
A 3'-oh, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases
Analyse A 3'-oh, 2',5'-phosphodiester substitution in the hairpin ribozyme active site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CQS
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 13-mer substrate strand with 3'-oh, 2',5'- phosphodiester covalently linking 5TH and 6TH…
- Ligands
- S9L, NCO
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 13-mer substrate strand with 3'-oh, 2',5'- phosphodiester covalently linking 5TH and 6TH nucleotides | rna | 13 | — | — |
| B | 29-mer ribozyme strand with S9L synthetic linker at 13TH position | rna | 29 | — | — |
| C | 19-mer ribozyme strand | rna | 19 | — | — |
Ligands and binding sites
- S9L · 2-[2-(2-hydroxyethoxy)ethoxy]ethyl dihydrogen phosphate · ligand · chains B, C
- NCO · Cobalt hexammine(iii) · ligand · chains B, C
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 | 203 | 0.44 | 0.74 | 18 | empty |
| 2 | 199 | 0.44 | 0.74 | 18 | empty |
| 3 | 152 | 0.40 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1002 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- A–B · 791 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–C · 334 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3CQS · A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals… · 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 3CQS · PDBe 3CQS
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