MolNFT v1 · #105688 · protein + RNA

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

4RCJ · Yth domain-containing family protein 1: “Crystal structure of YTHDF1 yth domain in complex with 5MER M6A RNA”. X-ray diffraction, 1 ligand (UNX). MolNFT v1 #105688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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

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