MolNFT v1 · #136772 · RNA

Co-crystal structure of the fluorogenic RNA mango

5V3F · RNA (31-mer): “Co-crystal structure of the fluorogenic RNA mango”. X-ray diffraction, 3 ligands (74G, K, PO4), 3 pockets (best druggability 0.51). MolNFT v1 #136772 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V3F
Type: RNA
Length: 50 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (31-mer)
Ligands: 74G, K, PO4
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (31-mer)	rna	31	—	—
B	RNA (31-mer)	rna	19	—	—

Ligands and binding sites

74G · 4-{[(2S)-3-{2,16-dioxo-20-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-2,3-dihydro-1,3-benzothiazol-2-yl]methyl}-1-methylquinolin-1-ium · ligand · 2 copies · chains A, B
K · Potassium ion · metal · 6 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains B

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

Pockets

3 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	293	0.51	0.75	24	K
2	104	0.33	0.73	8	74G
3	81	0.30	0.73	8	74G

Interfaces

1 interface between chains.

A–B · 639 Å² buried · 18 hydrogen bonds · nucleic-nucleic

Compared structures

5V3F · Co-crystal structure of the fluorogenic RNA Mango · 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 5V3F · PDBe 5V3F

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