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Crystal structure of the E. COLI thim riboswitch in complex with thiamine pyrophosphate, manganese 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: 7TDA
Type: RNA
Length: 79 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thim tpp riboswitch RNA (80-mer)
Ligands: TPP, MN, MG
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thim tpp riboswitch RNA (80-mer)	rna	79	—	—

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · chains A
MN · Manganese (II) ion · metal · 9 copies · chains A
MG · Magnesium ion · metal · 6 copies · 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	531	0.69	0.80	30	TPP, MN
2	88	0.31	0.73	16	MG
3	73	0.29	0.74	12	MN
4	85	0.29	0.72	13	MG

Modifications

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

Compared structures

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

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