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Crystal structure of the pepper aptamer in complex with hbc, cesium soak

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

PDB: 7EOJ
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, CS
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	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 · 9 copies · chains A
CS · Cesium ion · metal · 8 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	126	0.41	0.76	14	MG
2	146	0.38	0.73	19	MG
3	73	0.37	0.78	10	J8F

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

7EOJ · Crystal structure of the Pepper aptamer in complex with HBC, cesium 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 7EOJ · PDBe 7EOJ

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