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Structural basis for 2'-deoxyguanosine recognition by the 2'-dg-II class of riboswitches

Analyse Structural basis for 2'-deoxyguanosine recognition by the 2'-dg-II class of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P2H
Type: RNA
Length: 69 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (69-mer)
Ligands: NCO, GNG, MG
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (69-mer)	rna	69	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 5 copies · chains A
GNG · 2'-deoxy-guanosine · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	854	0.71	0.77	36	NCO, MG
2	233	0.49	0.76	16	NCO, MG
3	75	0.49	0.85	14	GNG

Modifications

Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).

Compared structures

6P2H · Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches · 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 6P2H · PDBe 6P2H

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