MolNFT v1 · #56183 · RNA

T. tengcongensis glms ribozyme bound to glucosamine-6-phosphate

2Z75 · Glms ribozyme substrate RNA: “T. tengcongensis glms ribozyme bound to glucosamine-6-phosphate”. X-ray diffraction, 2 ligands (GLP, MG), 4 pockets (best druggability 0.76). MolNFT v1 #56183 on GenesisL1: 3D structure, binding sites…

PDB: 2Z75
Type: RNA
Length: 143 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glms ribozyme substrate RNA; Glms ribozyme RNA
Ligands: GLP, 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	122	—	—

Ligands and binding sites

GLP · 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · chains A, B
MG · Magnesium ion · metal · 9 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	1097	0.76	0.79	60	MG
2	519	0.59	0.74	32	MG
3	220	0.50	0.77	22	GLP, MG
4	311	0.49	0.73	23	empty

Interfaces

1 interface between chains.

A–B · 1516 Å² buried · 101 hydrogen bonds · nucleic-nucleic

Compared structures

2Z75 · T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate · 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 2Z75 · PDBe 2Z75

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