SMTL ID : 6ktc.1

Crystal structure of YBX1 CSD with m5C RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x G- 5MC- C- U: RNA (5'-R(P*GP*(5MC)P*CP*U)-3')(Non-covalent)

G-5MC-C-U.1: 13 residues within 4Å: Chain A: W.15, N.17, N.20, Y.22, F.24, D.33, F.35, H.37, T.39, K.68, G.69, A.70, E.71 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.35, A:K.68 Hydrogen bonds: A:A.70 Water bridges: A:F.35, A:K.68 pi-Stacking: A:F.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zou, F. et al., DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-02-05

Peptides

Nuclease-sensitive element-binding protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nuclease-sensitive element-binding protein 1

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