MolNFT v1 · #145033 · RNA

Crystal structure of ykoy-mntp riboswitch chimera bound to cadmium

6CC3 · RNA (101-mer): “Crystal structure of ykoy-mntp riboswitch chimera bound to cadmium”. X-ray diffraction, 3 ligands (GTP, MG, CD), 6 pockets (best druggability 0.72). MolNFT v1 #145033 on GenesisL1: 3D structure, binding sites and…

PDB: 6CC3
Type: RNA
Length: 192 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (101-mer)
Ligands: GTP, MG, CD
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (101-mer)	rna	100	—	—
B	RNA (101-mer)	rna	92	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 16 copies · chains A, B
CD · Cadmium ion · metal · 12 copies · chains A, B

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

Pockets

6 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	939	0.72	0.77	52	CD, MG
2	1188	0.68	0.75	47	CD, MG
3	145	0.46	0.77	15	empty
4	94	0.43	0.80	14	empty
5	117	0.39	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 624 Å² buried · 26 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

6CC3 · Crystal structure of ykoY-mntP 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 6CC3 · PDBe 6CC3

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