Research workbench

Crystal structure of YTHDF1 yth domain in complex with 5MER M6A RNA

Analyse Crystal structure of YTHDF1 yth domain in complex with 5MER M6A RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RCJ
Type: protein + RNA
Length: 192 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yth domain-containing family protein 1; RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')
UniProt: Q9BYJ9
Ligands: UNX

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yth domain-containing family protein 1	protein	188	39% helix, 23% strand	Q9BYJ9
B	RNA (5'-R(GPGP(6MZ)PCP*U)-3')	rna	4	—	—

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.

Interfaces

1 interface between chains.

A–B · 578 Å² buried · 17 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

4RCJ · Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA · the same entry in another collection · chain B against B, TM-score 1.00
Q9BYJ9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 1 (Q9BYJ9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9BYJ9
Elsewhere: RCSB PDB 4RCJ · PDBe 4RCJ · UniProt Q9BYJ9

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