Research workbench

Structure of the arabidopsis thaliana thiamine pyrophosphate riboswitch with its regulatory ligand

Analyse Structure of the arabidopsis thaliana thiamine pyrophosphate riboswitch with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2CKY
Type: RNA
Length: 154 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleic acid
Ligands: TPP, OS, MG
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nucleic acid	rna	77	—	—

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
OS · Osmium ion · metal · 12 copies · chains A, B
MG · Magnesium ion · metal · 10 copies · chains A, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	595	0.71	0.80	27	MG, OS, TPP
2	553	0.67	0.79	26	MG, TPP, OS
3	332	0.51	0.74	18	OS
4	320	0.51	0.74	18	OS
5	219	0.46	0.74	19	MG, OS

Interfaces

1 interface between chains.

A–B · 38 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

2CKY · Structure of the Arabidopsis thaliana thiamine pyrophosphate riboswitch with its… · 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 2CKY · PDBe 2CKY

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