MolNFT v1 · #177540 · RNA

Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak

7ELP · NMT1_IR(46-mer): “Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak”. X-ray diffraction, 4 ligands (GTP, XAN, MG), 4 pockets (best druggability 0.53). MolNFT v1 #177540 on GenesisL1: 3D structure…

PDB: 7ELP
Type: RNA
Length: 90 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NMT1_IR(46-mer)
Ligands: GTP, XAN, MG, IR
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	NMT1_IR(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 · 16 copies · chains A, B
IR · Iridium ion · metal · 3 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	292	0.53	0.76	18	IR, MG
2	209	0.47	0.75	17	empty
3	174	0.45	0.76	19	IR, XAN, MG
4	81	0.31	0.74	16	IR, XAN, MG

Modifications

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

Compared structures

7ELP · Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak · 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 7ELP · PDBe 7ELP

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