MolNFT v1 · #145309 · RNA

Prpp riboswitch from T. mathranii bound to prpp

6CK5: “Prpp riboswitch from T. mathranii bound to prpp”. X-ray diffraction, 4 ligands (PRP, BA, MG), 9 pockets (best druggability 0.71). MolNFT v1 #145309 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6CK5
Type: RNA
Length: 208 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prpp riboswitch
Ligands: PRP, BA, MG, K
Pockets: 9 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Prpp riboswitch	rna	108	—	—
B	Prpp riboswitch	rna	100	—	—

Ligands and binding sites

PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
BA · Barium ion · metal · 20 copies · chains A, B
MG · Magnesium ion · metal · 8 copies · chains A, B
K · Potassium ion · metal · 3 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	644	0.71	0.80	38	BA, MG, K, PRP
2	659	0.70	0.79	40	BA, MG, PRP
3	476	0.65	0.78	30	BA
4	446	0.63	0.78	27	MG, K
5	350	0.58	0.77	28	BA

Interfaces

1 interface between chains.

A–B · 326 Å² buried · 8 hydrogen bonds · nucleic-nucleic

Compared structures

6CK5 · PRPP riboswitch from T. mathranii bound to PRPP · 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 6CK5 · PDBe 6CK5

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