MolNFT v1 · #110594 · RNA

Lactococcus lactis yybp-ykoy mn riboswitch bound to MN2+

4Y1I · Lactococcus lactis yybp-ykoy riboswitch: “Lactococcus lactis yybp-ykoy mn riboswitch bound to MN2+”. X-ray diffraction, 4 ligands (GTP, MG, BA), 7 pockets (best druggability 0.71). MolNFT v1 #110594 on GenesisL1: 3D structure…

PDB: 4Y1I
Type: RNA
Length: 200 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactococcus lactis yybp-ykoy riboswitch
Ligands: GTP, MG, BA, MN
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 25 copies · chains A, B
BA · Barium ion · metal · 19 copies · chains A, B
MN · Manganese (II) ion · metal · 3 copies · chains A, B

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

Pockets

7 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	863	0.71	0.77	48	MG, BA
2	1194	0.69	0.75	57	MG, BA
3	185	0.46	0.76	23	MG
4	176	0.43	0.75	18	MG, BA
5	118	0.37	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 207 Å² buried · 4 hydrogen bonds · nucleic-nucleic

Compared structures

4Y1I · Lactococcus lactis yybP-ykoY Mn riboswitch bound to 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 4Y1I · PDBe 4Y1I

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