MolNFT v1 · #78820 · RNA

Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'- deoxyguanosine, iridium hexammine soak

3SKL · RNA (66-mer): “Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'- deoxyguanosine, iridium hexammine soak”. X-ray diffraction, 3 ligands (IRI, GNG, MG), 3 pockets (best druggability 0.78). MolNFT v1 #78820 on…

PDB: 3SKL
Type: RNA
Length: 132 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (66-mer)
Ligands: IRI, GNG, MG
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (66-mer)	rna	66	—	—

Ligands and binding sites

IRI · Iridium hexammine ion · ligand · 10 copies · chains A, B
GNG · 2'-deoxy-guanosine · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 6 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	906	0.78	0.82	59	GNG, MG, IRI
2	416	0.67	0.81	33	GNG, MG
3	393	0.66	0.81	30	IRI

Interfaces

1 interface between chains.

A–B · 287 Å² buried · 5 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

3SKL · Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'-deoxyguanosine… · 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 3SKL · PDBe 3SKL

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