MolNFT v1 · #124174 · RNA

The structure of pistol ribozyme, soaked with MN2+

5K7E · RNA 47-mer: “The structure of pistol ribozyme, soaked with MN2+”. X-ray diffraction, 1 ligand (MN), 1 pocket (best druggability 0.66). MolNFT v1 #124174 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K7E
Type: RNA
Length: 58 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 47-mer; DNA/RNA 11-mer
Ligands: MN
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA 47-mer	rna	47	—	—
B	DNA/RNA 11-mer	rna	11	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	535	0.66	0.78	33	MN

Interfaces

1 interface between chains.

A–B · 666 Å² buried · 43 hydrogen bonds · nucleic-nucleic

Compared structures

5K7E · The structure of pistol ribozyme, soaked with Mn2+ · 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 5K7E · PDBe 5K7E

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