Research workbench

X-ray structure of a pseudouridine-containing yeast spliceosomal U2 snrna-intron branch site duplex bound to iodide ions

Analyse X-ray structure of a pseudouridine-containing yeast spliceosomal U2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CGP
Type: RNA
Length: 25 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*CP*GP*CP*GP*(PSU) P*AP*GP*UP*AP*GP*C)-3'); RNA (5'…
Ligands: IOD, SO4
Pockets: 1 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (5'-R(GPCPGPCPGP(PSU) PAPGPUPAPGPC)-3')	rna	12	—	—
B	RNA (5'- R(CPGPCPUPAPCPUPAPAPCPGPCP*G)-3')	rna	13	—	—

Ligands and binding sites

IOD · Iodide ion · ion · 3 copies · chains A, B
SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	284	0.49	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 544 Å² buried · 50 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3CGP · X-ray structure of a pseudouridine-containing yeast spliceosomal U2 snRNA-intron branch… · 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 3CGP · PDBe 3CGP

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