MolNFT v2 · #221760 · RNA

Structure of Mango III variant aptamer bound to T01-07M-B

8U5J: “Structure of Mango III variant aptamer bound to T01-07M-B”. X-ray diffraction at 1.7, 2 ligands (W6F, K), 1 pocket (best druggability 0.37). MolNFT v2 #221760 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8U5J
Type: RNA
Length: 36 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.7
Molecule: Mango III variant
Ligands: W6F, K
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · resolution 1.7 · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mango III variant	rna	36	—	—

Ligands and binding sites

W6F · 2-[(E)-(1,7-dimethylquinolin-4(1H)-ylidene)methyl]-3-{2,16-dioxo-20-[(3aR,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium · ligand · chains A
K · Potassium ion · metal · chains A
DMS · Dimethyl sulfoxide · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	71	0.37	0.79	9	W6F

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8U5J · PDBe 8U5J

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