MolNFT v1 · #101664 · RNA

Crystal structure of the E. COLI thim riboswitch in complex with (4- (1,2,3-thiadiazol-4-YL)PHENYL)METHANAMINE

4NYB · Thim tpp riboswitch: “Crystal structure of the E. COLI thim riboswitch in complex with (4- (1,2,3-thiadiazol-4-YL)PHENYL)METHANAMINE”. X-ray diffraction, 3 ligands (2QC, MG, MN), 3 pockets (best druggability 0.65). MolNFT v1 #101664…

PDB: 4NYB
Type: RNA
Length: 79 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thim tpp riboswitch
Ligands: 2QC, MG, MN
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thim tpp riboswitch	rna	79	—	—

Ligands and binding sites

2QC · 1-[4-(1,2,3-thiadiazol-4-yl)phenyl]methanamine · ligand · chains A
MG · Magnesium ion · metal · 9 copies · chains A
MN · Manganese (II) ion · metal · 4 copies · chains A

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

Pockets

3 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	482	0.65	0.78	34	2QC, MN
2	85	0.30	0.74	15	MG
3	52	0.21	0.71	11	MG

Modifications

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

Compared structures

4NYB · Crystal structure of the E. coli thiM riboswitch in complex with… · 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 4NYB · PDBe 4NYB

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