MolNFT v1 · #64050 · RNA

Class II ligase ribozyme product-template duplex, structure 2

3FS0 · 5'-R(*GP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3': “Class II ligase ribozyme product-template duplex, structure 2”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.23). MolNFT v1 #64050 on GenesisL1: 3D structure, binding sites…

PDB: 3FS0
Type: RNA
Length: 21 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*GP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'; 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*C)-3'
Ligands: MG
Pockets: 1 · best druggability 0.23

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-R(GPGPUPGPAPGPGPCPUPG)-3'	rna	10	—	—
B	5'-R(CPCPAPGPUPCPGPGPAPAP*C)-3'	rna	11	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 5 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	57	0.23	0.72	12	empty

Interfaces

1 interface between chains.

A–B · 545 Å² buried · 41 hydrogen bonds · nucleic-nucleic

Compared structures

3FS0 · Class II ligase ribozyme product-template duplex, structure 2 · 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 3FS0 · PDBe 3FS0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.