MolNFT v1 · #126310 · RNA

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

5LYV · 7SK RNA: “The crystal structure of 7SK 5'-hairpin - osmium derivative”. X-ray diffraction, 3 ligands (OHX, MG, CL), 8 pockets (best druggability 0.66). MolNFT v1 #126310 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LYV
Type: RNA
Length: 114 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 7SK RNA
Ligands: OHX, MG, CL
Pockets: 8 · 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

OHX · osmium (III) hexammine · ligand · chains A
MG · Magnesium ion · metal · chains B
CL · Chloride ion · ion · chains B

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

Pockets

8 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	453	0.66	0.79	30	empty
2	256	0.48	0.74	21	empty
3	201	0.47	0.76	22	MG
4	215	0.44	0.74	20	CL
5	83	0.35	0.76	10	empty

Interfaces

1 interface between chains.

A–B · 561 Å² buried · 10 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

5LYV · The crystal structure of 7SK 5'-hairpin - Osmium 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 5LYV · PDBe 5LYV

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