Research workbench
Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate
Analyse Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GDI
- Type
- RNA
- Length
- 160 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tpp riboswitch
- Ligands
- TPP, MG, K, NA
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y | Tpp riboswitch | rna | 80 | — | — |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains X, Y
- MG · Magnesium ion · metal · 6 copies · chains X, Y
- K · Potassium ion · metal · 3 copies · chains X
- NA · Sodium ion · metal · 2 copies · chains X
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 | 632 | 0.67 | 0.78 | 36 | NA, MG, TPP |
| 2 | 633 | 0.66 | 0.77 | 38 | MG, TPP |
| 3 | 227 | 0.43 | 0.73 | 21 | empty |
| 4 | 185 | 0.41 | 0.73 | 22 | empty |
| 5 | 135 | 0.35 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- X–Y · 160 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2GDI · Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine… · the same entry in another collection · chain X against X, 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 2GDI · PDBe 2GDI
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