MolNFT v1 · #78828 · RNA

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

3SKT · RNA (66-mer): “Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2'- deoxyguanosine, manganese soak”. X-ray diffraction, 3 ligands (GNG, MN, MG), 4 pockets (best druggability 0.75). MolNFT v1 #78828 on GenesisL1: 3D…

PDB: 3SKT
Type: RNA
Length: 132 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (66-mer)
Ligands: GNG, MN, MG
Pockets: 4 · best druggability 0.75

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

GNG · 2'-deoxy-guanosine · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 10 copies · chains A, B
MG · Magnesium ion · metal · 9 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	595	0.75	0.83	38	GNG, MN, MG
2	1113	0.74	0.78	56	MN
3	437	0.70	0.82	30	MG
4	174	0.55	0.81	19	GNG

Interfaces

1 interface between chains.

A–B · 325 Å² buried · 7 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3SKT · 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 3SKT · PDBe 3SKT

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