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Crystal structure of the Pepper aptamer in complex with HBC497

Analyse Crystal structure of the Pepper aptamer in complex with HBC497 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EOL
Type: RNA
Length: 48 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.309
Source: synthetic construct
Molecule: Pepper (49-MER)
Ligands: GTP, J8O, MG
Pockets: 3 · best druggability 0.41

Structure

x-ray diffraction · resolution 2.309 · 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
J8O · 4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl) amino]pyrazin-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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	189	0.41	0.74	20	empty
2	77	0.39	0.79	10	J8O
3	55	0.28	0.75	11	MG

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7EOL · Crystal structure of the pepper aptamer in complex with HBC497 · 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 7EOL · PDBe 7EOL

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