MolNFT v1 · #145001 · RNA

Crystal structure of the L.LACTIS ykoy riboswitch bound to cadmium

6CB3 · RNA (99-mer): “Crystal structure of the L.LACTIS ykoy riboswitch bound to cadmium”. X-ray diffraction, 4 ligands (GTP, CD, BA), 9 pockets (best druggability 0.70). MolNFT v1 #145001 on GenesisL1: 3D structure, binding sites and…

PDB: 6CB3
Type: RNA
Length: 198 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (99-mer)
Ligands: GTP, CD, BA, MG
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (99-mer)	rna	99	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
CD · Cadmium ion · metal · 38 copies · chains A, B
BA · Barium ion · metal · 13 copies · chains A, B
MG · Magnesium ion · metal · 6 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	835	0.70	0.77	51	CD, BA, MG
2	737	0.68	0.77	37	CD, BA, MG
3	166	0.46	0.76	16	empty
4	144	0.44	0.77	15	empty
5	99	0.37	0.76	13	CD

Interfaces

1 interface between chains.

A–B · 341 Å² buried · 5 hydrogen bonds · nucleic-nucleic

Compared structures

6CB3 · Crystal structure of the L.Lactis YkoY riboswitch bound to cadmium · 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 6CB3 · PDBe 6CB3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.