MolNFT v1 · #110595 · RNA

Lactococcus lactis yybp-ykoy mn riboswitch A41U binding site mutant in presence of MN2+

4Y1J · Yybp-ykoy riboswitch: “Lactococcus lactis yybp-ykoy mn riboswitch A41U binding site mutant in presence of MN2+”. X-ray diffraction, 3 ligands (GTP, SR, MG), 9 pockets (best druggability 0.72). MolNFT v1 #110595 on GenesisL1: 3D…

PDB: 4Y1J
Type: RNA
Length: 200 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yybp-ykoy riboswitch
Ligands: GTP, SR, MG
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yybp-ykoy riboswitch	rna	100	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
SR · Strontium ion · metal · 52 copies · chains A, B
MG · Magnesium ion · metal · 24 copies · chains A, B

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

Pockets

9 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	1057	0.72	0.77	55	SR, MG
2	791	0.69	0.77	45	SR, MG
3	367	0.56	0.76	25	empty
4	177	0.48	0.77	16	SR
5	126	0.39	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 138 Å² buried · 4 hydrogen bonds · nucleic-nucleic

Compared structures

4Y1J · Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+ · 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 4Y1J · PDBe 4Y1J

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