Research workbench
Crystal structure of the pepper aptamer in complex with HBC620
Analyse Crystal structure of the pepper aptamer in complex with HBC620 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EOP
- 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, J93, 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
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- J93 · 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl) amino]thieno[3,2-b]thiophen-2-yl]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 | 170 | 0.41 | 0.74 | 20 | empty |
| 2 | 73 | 0.36 | 0.78 | 8 | J93 |
| 3 | 54 | 0.27 | 0.75 | 11 | MG |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7EOP · Crystal structure of the Pepper aptamer in complex with HBC620 · 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 7EOP · PDBe 7EOP
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