MolNFT v1 · #39244 · RNA

Pre-cleavage state of the thermoanaerobacter tengcongensis glms ribozyme bound to glucose-6-phosphate

2HO7 · Glms ribozyme substrate RNA: “Pre-cleavage state of the thermoanaerobacter tengcongensis glms ribozyme bound to glucose-6-phosphate”. X-ray diffraction, 2 ligands (G6P, MG), 4 pockets (best druggability 0.76). MolNFT v1 #39244 on…

PDB: 2HO7
Type: RNA
Length: 144 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glms ribozyme substrate RNA; Glms ribozyme RNA
Ligands: G6P, MG
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glms ribozyme substrate RNA	rna	21	—	—
B	Glms ribozyme RNA	rna	123	—	—

Ligands and binding sites

G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · chains A, B
MG · Magnesium ion · metal · 4 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1086	0.76	0.79	60	MG
2	411	0.61	0.78	26	G6P, MG
3	409	0.54	0.74	27	MG
4	287	0.47	0.73	22	empty

Interfaces

1 interface between chains.

A–B · 1504 Å² buried · 116 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

2HO7 · Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme bound to… · 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 2HO7 · PDBe 2HO7

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