Research workbench
Structure of the eukaryotic tpp-specific riboswitch bound to the antibacterial compound pyrithiamine pyrophosphate
Analyse Structure of the eukaryotic tpp-specific riboswitch bound to the antibacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D2V
- Type
- RNA
- Length
- 154 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tpp-specific riboswitch
- Ligands
- PYI, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tpp-specific riboswitch | rna | 77 | — | — |
Ligands and binding sites
- PYI · 1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-(2-{[hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-methylpyridinium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.79 | 0.81 | 62 | PYI, MG |
| 2 | 293 | 0.50 | 0.74 | 18 | empty |
| 3 | 276 | 0.47 | 0.73 | 30 | MG |
| 4 | 243 | 0.43 | 0.72 | 18 | empty |
| 5 | 139 | 0.41 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 335 Ų buried · 10 hydrogen bonds · nucleic-nucleic
Compared structures
- 3D2V · Structure of the eukaryotic TPP-specific riboswitch bound to the antibacterial compound… · 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 3D2V · PDBe 3D2V
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