MolNFT v1 · #64120 · RNA
Cocrystal structure of a class-I PREQ1 riboswitch
3FU2: “Cocrystal structure of a class-I PREQ1 riboswitch”. X-ray diffraction, 2 ligands (PRF, CA), 3 pockets (best druggability 0.49). MolNFT v1 #64120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FU2
- Type
- RNA
- Length
- 94 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PREQ1 riboswitch
- Ligands
- PRF, CA
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | PREQ1 riboswitch | rna | 31 | — | — |
| B | PREQ1 riboswitch | rna | 32 | — | — |
Ligands and binding sites
- PRF · 7-deaza-7-aminomethyl-guanine · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 9 copies · chains A, 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 | 121 | 0.49 | 0.81 | 15 | PRF, CA |
| 2 | 97 | 0.44 | 0.80 | 14 | PRF, CA |
| 3 | 119 | 0.44 | 0.78 | 15 | PRF, CA |
Interfaces
2 interfaces between chains.
- A–B · 261 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–C · 18 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 3FU2 · Cocrystal structure of a class-I preQ1 riboswitch · 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 3FU2 · PDBe 3FU2
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