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Crystal structure of thf riboswitch, bound with 5-formyl-thf

Analyse Crystal structure of thf riboswitch, bound with 5-formyl-thf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SUH
Type: RNA
Length: 101 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Riboswitch
Ligands: FFO, NA
Pockets: 5 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Riboswitch	rna	101	—	—

Ligands and binding sites

FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · chains X
NA · Sodium ion · metal · 2 copies · chains X

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	358	0.55	0.75	25	empty
2	368	0.51	0.73	22	empty
3	276	0.48	0.74	22	NA
4	164	0.44	0.76	14	empty
5	110	0.39	0.76	11	empty

Modifications

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

Compared structures

3SUH · Crystal structure of THF riboswitch, bound with 5-formyl-THF · the same entry in another collection · chain X against X, 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 3SUH · PDBe 3SUH

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