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Crystal structure of the DOMAIN1 of NAD+ riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in MN2+

Analyse Crystal structure of the DOMAIN1 of NAD+ riboswitch with nicotinamide adenine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D7Z
Type: RNA
Length: 51 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18GAAA(52-mer)
Ligands: GTP, NAD, MN, MG
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	18GAAA(52-mer)	rna	51	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A
NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
MN · Manganese (II) ion · metal · 16 copies · chains A
MG · Magnesium ion · metal · 11 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	507	0.54	0.72	29	MG, MN

Compared structures

7D7Z · Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine… · 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 7D7Z · PDBe 7D7Z

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