MolNFT v1 · #126307 · RNA

The crystal structure of 7SK 5'-hairpin - gold derivative

5LYS · 7SK RNA: “The crystal structure of 7SK 5'-hairpin - gold derivative”. X-ray diffraction, 3 ligands (AU, MG, NA), 10 pockets (best druggability 0.66). MolNFT v1 #126307 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LYS
Type: RNA
Length: 114 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 7SK RNA
Ligands: AU, MG, NA
Pockets: 10 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	7SK RNA	rna	57	—	—

Ligands and binding sites

AU · Gold ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · chains B
NA · Sodium ion · metal · chains B

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

Pockets

10 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	464	0.66	0.79	30	NA
2	205	0.44	0.74	19	empty
3	170	0.40	0.74	17	empty
4	83	0.36	0.77	10	MG
5	106	0.36	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 558 Å² buried · 9 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

5LYS · The crystal structure of 7SK 5'-hairpin - Gold derivative · 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 5LYS · PDBe 5LYS

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