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Crystal structure of xanthine riboswitch with xanthine, manganese saok

Analyse Crystal structure of xanthine riboswitch with xanthine, manganese saok in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ELQ
Type: RNA
Length: 90 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NMT1_MN (46-mer)
Ligands: GTP, XAN, MG, MN
Pockets: 4 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	NMT1_MN (46-mer)	rna	45	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
XAN · Xanthine · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 9 copies · chains A, B
MN · Manganese (II) ion · metal · 8 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	206	0.46	0.75	17	MG
2	164	0.41	0.74	18	MG
3	120	0.39	0.76	14	XAN, MN
4	107	0.36	0.75	18	XAN, MN, MG

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7ELQ · Crystal structure of xanthine riboswitch with xanthine, manganese saok · 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 7ELQ · PDBe 7ELQ

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