Research workbench

Crystal structure of an active group I ribozyme-product complex

Analyse Crystal structure of an active group I ribozyme-product complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Y0Q
Type: RNA
Length: 233 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group I ribozyme; 5'-R(*GP*CP*UP*U)-3'
Ligands: SPK, MG, SO4
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group I ribozyme	rna	229	—	—
B	5'-R(GPCPUPU)-3'	rna	4	—	—

Ligands and binding sites

SPK · Spermine (fully protonated form) · ligand · chains A
MG · Magnesium ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	899	0.76	0.80	49	MG
2	762	0.70	0.78	46	MG
3	696	0.62	0.74	38	empty
4	603	0.60	0.74	35	empty
5	64	0.52	0.87	15	empty

Interfaces

1 interface between chains.

A–B · 455 Å² buried · 32 hydrogen bonds · nucleic-nucleic

Compared structures

1Y0Q · Crystal structure of an active group I ribozyme-product complex · 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 1Y0Q · PDBe 1Y0Q

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.