MolNFT v1 · #177631 · RNA
Crystal structure of the pepper aptamer in complex with HBC514
7EON · Pepper (49-mer): “Crystal structure of the pepper aptamer in complex with HBC514”. X-ray diffraction, 3 ligands (GTP, J8U, MG), 3 pockets (best druggability 0.39). MolNFT v1 #177631 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7EON
- Type
- RNA
- Length
- 48 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pepper (49-mer)
- Ligands
- GTP, J8U, MG
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pepper (49-mer) | rna | 48 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- J8U · 4-[(~{Z})-1-cyano-2-[4-[2-(dimethylamino)ethyl-methyl-amino]phenyl]ethenyl]benzenecarbonitrile · ligand · chains A
- MG · Magnesium ion · metal · 5 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.39 | 0.73 | 20 | empty |
| 2 | 75 | 0.38 | 0.79 | 10 | J8U |
| 3 | 52 | 0.27 | 0.75 | 11 | MG |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7EON · Crystal structure of the Pepper aptamer in complex with HBC514 · 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 7EON · PDBe 7EON
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.