MolNFT v1 · #177543 · RNA
Crystal structure of xanthine riboswitch with 8-azaxanthine
7ELS · NMT1_8-azaxanthine (46-mer): “Crystal structure of xanthine riboswitch with 8-azaxanthine”. X-ray diffraction, 3 ligands (GTP, AZA, MG), 4 pockets (best druggability 0.52). MolNFT v1 #177543 on GenesisL1: 3D structure, binding sites…
- PDB
- 7ELS
- Type
- RNA
- Length
- 90 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NMT1_8-azaxanthine (46-mer)
- Ligands
- GTP, AZA, MG
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NMT1_8-azaxanthine (46-mer) | rna | 45 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- AZA · 8-azaxanthine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 13 copies · chains A, B
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 | 277 | 0.52 | 0.76 | 18 | MG |
| 2 | 220 | 0.46 | 0.74 | 17 | MG |
| 3 | 126 | 0.42 | 0.77 | 13 | MG, AZA |
| 4 | 89 | 0.38 | 0.78 | 14 | MG, AZA |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7ELS · Crystal structure of xanthine riboswitch with 8-azaxanthine · 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 7ELS · PDBe 7ELS
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