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

Analyse Crystal structure of the E. COLI thim riboswitch in complex with thiamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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

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