MolNFT v1 · #146598 · RNA

Ppgpp riboswitch bound to ppgpp, native structure

6DMC: “Ppgpp riboswitch bound to ppgpp, native structure”. X-ray diffraction, 4 ligands (G4P, MG, NA), 10 pockets (best druggability 0.65). MolNFT v1 #146598 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DMC
Type: RNA
Length: 204 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ppgpp riboswitch
Ligands: G4P, MG, NA, K
Pockets: 10 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ppgpp riboswitch	rna	102	—	—

Ligands and binding sites

G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 21 copies · chains A, B
NA · Sodium ion · metal · 10 copies · chains A, B
K · Potassium ion · metal · chains A

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	495	0.65	0.78	33	NA
2	607	0.62	0.75	34	NA
3	489	0.55	0.73	31	G4P, MG
4	343	0.51	0.74	31	MG, NA, K
5	207	0.47	0.76	21	G4P, MG

Interfaces

1 interface between chains.

A–B · 586 Å² buried · 13 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

6DMC · ppGpp Riboswitch bound to ppGpp, native structure · 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 6DMC · PDBe 6DMC

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