Research workbench
Crystal structure of the E. COLI thim riboswitch in complex with thiamine
Analyse Crystal structure of the E. COLI thim riboswitch in complex with thiamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NYG
- Type
- RNA
- Length
- 77 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thim tpp riboswitch
- Ligands
- VIB, MG
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thim tpp riboswitch | rna | 77 | — | — |
Ligands and binding sites
- VIB · 3-(4-amino-2-methyl-pyrimidin-5-ylmethyl)-5-(2-hydroxy-ethyl)-4-methyl-thiazol-3-ium · ligand · chains A
- MG · Magnesium ion · metal · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.66 | 0.77 | 28 | VIB, MG |
| 2 | 102 | 0.32 | 0.73 | 16 | empty |
| 3 | 91 | 0.30 | 0.73 | 12 | empty |
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4NYG · Crystal structure of the E. coli thiM riboswitch in complex with thiamine · 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 4NYG · PDBe 4NYG
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