MolNFT v1 · #36791 · RNA
Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (G8DAP, U39C) at pH 8.6
2FGP · 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3': “Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (G8DAP, U39C) at pH 8.6”. X-ray diffraction, 1 ligand (NCO), 3 pockets (best druggability 0.41). MolNFT v1…
- PDB
- 2FGP
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'…
- Ligands
- NCO
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3' | rna | 13 | — | — |
| B | 5'-R(*CP*GP*GP*UP*GP*AP*(N6G)P*AP*AP*GP*GP*G)-3' | rna | 12 | — | — |
| C | 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)- 3' | rna | 17 | — | — |
| D | 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 · chains C, D
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 | 188 | 0.41 | 0.74 | 16 | NCO |
| 2 | 173 | 0.41 | 0.74 | 20 | empty |
| 3 | 125 | 0.37 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 888 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–B · 679 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–D · 337 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- B–C · 203 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- A–C · 174 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2FGP · Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c)… · 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 2FGP · PDBe 2FGP
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.