MolNFT v1 · #124172 · RNA

The native structure of native pistol ribozyme

5K7C · RNA 47-mer: “The native structure of native pistol ribozyme”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.67). MolNFT v1 #124172 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K7C
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: MG
Pockets: 1 · best druggability 0.67

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

MG · Magnesium ion · metal · 3 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	595	0.67	0.78	35	MG

Interfaces

1 interface between chains.

A–B · 683 Å² buried · 44 hydrogen bonds · nucleic-nucleic

Compared structures

5K7C · The native structure of native pistol ribozyme · 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 5K7C · PDBe 5K7C

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