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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with N6-methyl-adenosine-5'-triphosphate (M6ATP)

Analyse Crystal structure of the ADP-binding domain of the NAD+ riboswitch with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TFE
Type: RNA
Length: 52 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chains: a
Ligands: N6E, MG, NA, BR
Pockets: 1 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chains: a	rna	52	—	—

Ligands and binding sites

N6E · N6-Methyladenosine 5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · 10 copies · chains A
NA · Sodium ion · metal · 4 copies · chains A
BR · Bromide ion · ion · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	551	0.56	0.72	30	MG, BR, NA

Compared structures

6TFE · Crystal structure of the ADP-binding domain of the NAD+ riboswitch with… · 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 6TFE · PDBe 6TFE

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