MolNFT v1 · #101669 · RNA
Crystal structure of the E. COLI thim riboswitch in complex with thiamine
4NYG · Thim tpp riboswitch: “Crystal structure of the E. COLI thim riboswitch in complex with thiamine”. X-ray diffraction, 2 ligands (VIB, MG), 3 pockets (best druggability 0.66). MolNFT v1 #101669 on GenesisL1: 3D structure, binding…
- 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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