MolNFT v1 · #188134 · RNA

Crystal structure of the E. COLI thim riboswitch in complex with thiamine bisphosphonate, calcium ions

7TDC · Thim riboswitch RNA (83-mer): “Crystal structure of the E. COLI thim riboswitch in complex with thiamine bisphosphonate, calcium ions”. X-ray diffraction, 3 ligands (GMI, MG, CA), 4 pockets (best druggability 0.70). MolNFT v1…

PDB: 7TDC
Type: RNA
Length: 79 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thim riboswitch RNA (83-mer)
Ligands: GMI, MG, CA
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thim riboswitch RNA (83-mer)	rna	79	—	—

Ligands and binding sites

GMI · [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic acid · ligand · chains A
MG · Magnesium ion · metal · 4 copies · chains A
CA · Calcium ion · metal · chains A

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

Pockets

4 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	508	0.70	0.81	30	GMI, CA, MG
2	98	0.33	0.74	14	MG
3	109	0.32	0.72	12	empty
4	68	0.27	0.73	13	empty

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

7TDC · Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate… · 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 7TDC · PDBe 7TDC

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