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An escherichia COLI yybp-ykoy mn riboswitch in the MN2+-free state

Analyse An escherichia COLI yybp-ykoy mn riboswitch in the MN2+-free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Y1M
Type: RNA
Length: 183 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E. COLI yybp-ykoy riboswitch
Ligands: GTP, SR, MG
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	E. COLI yybp-ykoy riboswitch	rna	107	—	—
A	E. COLI yybp-ykoy riboswitch	rna	76	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains B, A
SR · Strontium ion · metal · 65 copies · chains B, A
MG · Magnesium ion · metal · 9 copies · chains B, A

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1069	0.68	0.74	54	SR
2	549	0.60	0.75	31	SR, MG
3	74	0.54	0.87	14	SR
4	119	0.42	0.77	17	SR
5	178	0.38	0.72	19	SR

Interfaces

1 interface between chains.

B–A · 439 Å² buried · 13 hydrogen bonds · nucleic-nucleic

Compared structures

4Y1M · An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state · the same entry in another collection · chain B against B, 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 4Y1M · PDBe 4Y1M

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