Research workbench

The crystal structure of an RNA complex

Analyse The crystal structure of an RNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R3I
Type: protein + RNA
Length: 169 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing protein 1; RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')
UniProt: Q96MU7
Ligands: UNX
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yth domain-containing protein 1	protein	164	34% helix, 26% strand	Q96MU7
B	RNA (5'-R(GPGP(6MZ)PCP*U)-3')	rna	5	—	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 7 copies · chains A, B

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	50	0.35	0.79	14	empty

Interfaces

1 interface between chains.

A–B · 820 Å² buried · 19 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

4R3I · The crystal structure of an RNA 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
Every structure of UniProt Q96MU7
Elsewhere: RCSB PDB 4R3I · PDBe 4R3I · UniProt Q96MU7

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