Research workbench
PREQ1-II riboswitch with an engineered G-U wobble pair bound to cs+
Analyse PREQ1-II riboswitch with an engineered G-U wobble pair bound to cs+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D5L
- Type
- RNA
- Length
- 308 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PREQ1-II riboswitch
- Ligands
- PRF, CS, MG
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | PREQ1-II riboswitch | rna | 77 | — | — |
Ligands and binding sites
- PRF · 7-deaza-7-aminomethyl-guanine · ligand · 4 copies · chains A, B, C, D
- CS · Cesium ion · metal · 32 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.77 | 0.80 | 55 | empty |
| 2 | 1139 | 0.73 | 0.78 | 59 | CS |
| 3 | 671 | 0.73 | 0.80 | 38 | empty |
| 4 | 916 | 0.72 | 0.77 | 44 | MG |
| 5 | 193 | 0.50 | 0.78 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 324 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- B–D · 285 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- A–C · 278 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- A–B · 91 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5D5L · PreQ1-II riboswitch with an engineered G-U wobble pair bound to Cs+ · 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 5D5L · PDBe 5D5L
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