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An all-RNA hairpin ribozyme A38N1DA variant with a product mimic substrate strand

Analyse An all-RNA hairpin ribozyme A38N1DA variant with a product mimic substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GS5
Type: RNA
Length: 61 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (25-mer); RNA (36-mer)
Ligands: NCO, S9L, SO4
Pockets: 3 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (25-mer)	rna	25	—	—
C	RNA (36-mer)	rna	36	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains C, A
S9L · 2-[2-(2-hydroxyethoxy)ethoxy]ethyl dihydrogen phosphate · ligand · chains A, C
SO4 · Sulfate ion · ion · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	197	0.41	0.73	18	empty
2	170	0.40	0.74	15	empty
3	139	0.37	0.73	18	empty

Interfaces

1 interface between chains.

A–C · 703 Å² buried · 28 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

3GS5 · An all-RNA hairpin ribozyme A38N1dA variant with a product mimic substrate strand · 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 3GS5 · PDBe 3GS5

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