MolNFT v1 · #58483 · RNA
Minimally junctioned hairpin ribozyme incorporates A38G mutation and a 2',5'-phosphodiester linkage at the active site
3B58 · Loop a substrate strand: “Minimally junctioned hairpin ribozyme incorporates A38G mutation and a 2',5'-phosphodiester linkage at the…”. X-ray diffraction, 3 ligands (NCO, S9L, SO4), 3 pockets (best druggability 0.44). MolNFT v1…
- PDB
- 3B58
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Loop a substrate strand; 29-mer loop a and loop B ribozyme strand; Loop B S-turn strand
- 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 | Loop a substrate strand | rna | 13 | — | — |
| B | 29-mer loop a and loop B ribozyme strand | rna | 29 | — | — |
| C | Loop B S-turn strand | rna | 19 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains A, B, C
- S9L · 2-[2-(2-hydroxyethoxy)ethoxy]ethyl dihydrogen phosphate · ligand · chains B, C
- 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 | 201 | 0.44 | 0.74 | 17 | empty |
| 2 | 182 | 0.41 | 0.74 | 20 | empty |
| 3 | 185 | 0.41 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 994 Ų buried · 79 hydrogen bonds · nucleic-nucleic
- A–B · 799 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–C · 325 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3B58 · Minimally Junctioned Hairpin Ribozyme Incorporates A38G Mutation and a… · the same entry in another collection · chain C against C, 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 3B58 · PDBe 3B58
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