Research workbench
Crystal structure of an E. COLI thi-box riboswitch bound to benfotiamine
Analyse Crystal structure of an E. COLI thi-box riboswitch bound to benfotiamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HOO
- Type
- RNA
- Length
- 83 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thi-box riboswitch
- Ligands
- BFT, CA
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thi-box riboswitch | rna | 83 | — | — |
Ligands and binding sites
- BFT · S-benzoylthiamine O-monophosphate · ligand · chains A
- CA · Calcium ion · metal · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.68 | 0.79 | 29 | CA, BFT |
| 2 | 136 | 0.38 | 0.74 | 16 | CA |
| 3 | 68 | 0.32 | 0.76 | 11 | empty |
| 4 | 98 | 0.31 | 0.72 | 11 | empty |
Compared structures
- 2HOO · Crystal structure of an E. coli thi-box riboswitch bound to benfotiamine · 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 2HOO · PDBe 2HOO
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