SMTL ID : 7f3i.1

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-trimer

Ligands

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

G-U-5MC-U-5MC.1: 19 residues within 4Å: Chain A: K.15, W.16, F.17, N.18, V.19, R.20, N.21, Y.23, F.25, D.34, F.36, H.38, K.69, G.70, A.71, E.72, Y.89 Chain C: K.15, W.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.89 Hydrogen bonds: A:F.17, A:N.18, A:V.19, A:R.20, A:N.21 pi-Stacking: A:Y.89 G-U-5MC-U-5MC.2: 22 residues within 4Å: Chain B: W.16, F.17, N.18, V.19, R.20, N.21, Y.23, F.25, D.34, F.36, H.38, T.40, K.69, G.70, A.71, E.72, Y.89 Chain C: R.20, N.21, Q.39, F.50, L.51 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.89 Hydrogen bonds: B:F.17, B:N.18, B:V.19, B:R.20, B:N.21, C:Q.39, C:Q.39 Water bridges: B:F.17, B:F.17, C:R.52, C:R.52 pi-Stacking: B:Y.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P212121. To Be Published

Release Date

2022-06-22

Peptides

Y-box-binding protein 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

Y-box-binding protein 2

Related Entries With Identical Sequence