MolNFT v1 · #188132 · RNA

Crystal structure of the E. COLI thim riboswitch in complex with thiamine pyrophosphate, manganese ions

7TDA · Thim tpp riboswitch RNA (80-mer): “Crystal structure of the E. COLI thim riboswitch in complex with thiamine pyrophosphate, manganese ions”. X-ray diffraction, 3 ligands (TPP, MN, MG), 4 pockets (best druggability 0.69). MolNFT v1…

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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