Research workbench
An all-RNA hairpin ribozyme with mutation A38N1DA
Analyse An all-RNA hairpin ribozyme with mutation A38N1DA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GS1
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'); RNA…
- Ligands
- NCO, S9L, SO4
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (5'- R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3') | rna | 13 | — | — |
| B | RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)- 3') | rna | 12 | — | — |
| C | RNA (5'- R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3') | rna | 17 | — | — |
| D | RNA (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 C, D, A, B
- S9L · 2-[2-(2-hydroxyethoxy)ethoxy]ethyl dihydrogen phosphate · ligand · chains 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 | 215 | 0.43 | 0.74 | 16 | empty |
| 2 | 189 | 0.41 | 0.73 | 19 | empty |
| 3 | 161 | 0.39 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 883 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- A–B · 654 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- A–D · 338 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- B–C · 199 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- A–C · 175 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3GS1 · An all-RNA Hairpin Ribozyme with mutation A38N1dA · the same entry in another collection · chain D against D, 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 3GS1 · PDBe 3GS1
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