Research workbench
Crystal structure of the pepper aptamer in complex with hbc, iridium hexammine soak
Analyse Crystal structure of the pepper aptamer in complex with hbc, iridium hexammine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EOG
- Type
- RNA
- Length
- 48 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pepper (49-mer)
- Ligands
- IRI, GTP, J8F, MG
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pepper (49-mer) | rna | 48 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 3 copies · chains A
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- 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 | 183 | 0.41 | 0.73 | 20 | empty |
| 2 | 73 | 0.37 | 0.79 | 10 | J8F |
| 3 | 53 | 0.27 | 0.75 | 11 | MG |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7EOG · Crystal structure of the Pepper aptamer in complex with HBC, iridium hexammine soak · 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 7EOG · PDBe 7EOG
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