Research workbench
Crystal structure of the pepper aptamer in complex with hbc
Analyse Crystal structure of the pepper aptamer in complex with hbc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EOH
- Type
- RNA
- Length
- 49 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pepper (49-mer)
- Ligands
- J8F, MG
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pepper (49-mer) | rna | 49 | — | — |
Ligands and binding sites
- J8F · 4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(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 | 120 | 0.40 | 0.76 | 14 | MG |
| 2 | 163 | 0.39 | 0.73 | 20 | empty |
| 3 | 79 | 0.38 | 0.78 | 11 | J8F |
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7EOH · Crystal structure of the Pepper aptamer in complex with HBC · 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 7EOH · PDBe 7EOH
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