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

Analyse Pre-cleavage state of the thermoanaerobacter tengcongensis glms ribozyme bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2H0Z
Type: RNA
Length: 144 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glms ribozyme deoxy RNA inhibitor; 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 deoxy RNA inhibitor	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 · 8 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	1089	0.76	0.79	59	MG
2	519	0.59	0.74	33	MG
3	339	0.59	0.78	25	G6P, MG
4	318	0.50	0.74	24	empty

Interfaces

1 interface between chains.

A–B · 1507 Å² buried · 110 hydrogen bonds · nucleic-nucleic

Compared structures

2H0Z · 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

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2H0Z · PDBe 2H0Z

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