MolNFT v1 · #126309 · RNA

The native crystal structure of 7SK 5'-hairpin

5LYU · 7SK RNA: “The native crystal structure of 7SK 5'-hairpin”. X-ray diffraction, 3 ligands (NA, MG, CL), 9 pockets (best druggability 0.60). MolNFT v1 #126309 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LYU
Type: RNA
Length: 116 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 7SK RNA
Ligands: NA, MG, CL
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	7SK RNA	rna	58	—	—

Ligands and binding sites

NA · Sodium ion · metal · chains A
MG · Magnesium ion · metal · chains B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	295	0.60	0.80	25	empty
2	179	0.55	0.81	13	empty
3	328	0.50	0.74	25	empty
4	314	0.49	0.73	24	empty
5	208	0.48	0.77	22	NA, MG

Interfaces

1 interface between chains.

A–B · 568 Å² buried · 10 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

5LYU · The native crystal structure of 7SK 5'-hairpin · 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 5LYU · PDBe 5LYU

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