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Co-crystal structure of the fluorogenic mango-IV homodimer bound to TO1-biotin

Analyse Co-crystal structure of the fluorogenic mango-IV homodimer bound to TO1-biotin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V9D
Type: RNA
Length: 55 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (28-mer)
Ligands: QW4, K, BR
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	RNA (28-mer)	rna	28	—	—
E	RNA (28-mer)	rna	27	—	—

Ligands and binding sites

QW4 · 2-[(E)-(1-methylquinolin-4(1H)-ylidene)methyl]-3-(2-oxopropyl)-1,3-benzothiazol-3-ium · ligand · 3 copies · chains B, E
K · Potassium ion · metal · 4 copies · chains B, E
BR · Bromide ion · ion · 2 copies · chains B, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	193	0.44	0.74	10	QW4
2	176	0.41	0.74	10	QW4
3	66	0.26	0.73	14	BR

Interfaces

1 interface between chains.

B–E · 504 Å² buried · 43 hydrogen bonds · nucleic-nucleic

Compared structures

6V9D · Co-crystal structure of the fluorogenic Mango-IV homodimer bound to TO1-Biotin · the same entry in another collection · chain B against B, 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 6V9D · PDBe 6V9D

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