MolNFT v1 · #145031 · RNA

Crystal structure of ykoy-alx riboswitch chimera bound to cadmium

6CC1 · RNA (94-mer): “Crystal structure of ykoy-alx riboswitch chimera bound to cadmium”. X-ray diffraction, 4 ligands (GTP, CD, BA), 7 pockets (best druggability 0.73). MolNFT v1 #145031 on GenesisL1: 3D structure, binding sites and…

PDB: 6CC1
Type: RNA
Length: 192 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (94-mer)
Ligands: GTP, CD, BA, MG
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (94-mer)	rna	93	—	—
B	RNA (94-mer)	rna	99	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
CD · Cadmium ion · metal · 23 copies · chains A, B
BA · Barium ion · metal · 8 copies · chains A, B
MG · Magnesium ion · metal · chains A

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	880	0.73	0.78	40	CD, BA
2	883	0.71	0.77	50	CD, BA
3	153	0.47	0.77	14	empty
4	306	0.46	0.72	31	CD, BA
5	134	0.43	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 125 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6CC1 · Crystal structure of ykoY-alx riboswitch chimera 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 6CC1 · PDBe 6CC1

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