MolNFT v1 · #164977 · RNA

Crystal structure of the ADP-binding domain of the NAD+ riboswitch with nicotinamide adenine dinucleotide, reduced (NADH); soaking with MANGANESE(II) (MN2+)

6TFH · Chains: a: “Crystal structure of the ADP-binding domain of the NAD+ riboswitch with nicotinamide adenine dinucleotide…”. X-ray diffraction, 3 ligands (NAD, MN, NA), 1 pocket (best druggability 0.61). MolNFT v1 #164977 on GenesisL1…

PDB: 6TFH
Type: RNA
Length: 52 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chains: a
Ligands: NAD, MN, NA
Pockets: 1 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
MN · Manganese (II) ion · metal · 9 copies · chains A
NA · Sodium ion · metal · 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	694	0.61	0.73	30	MN

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

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

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