SMTL ID : 7f3k.1

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P21212

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x U- C- A- U- 5MC- U: RNA (5'-R(*UP*CP*AP*UP*(5MC)P*U)-3')(Non-covalent)

U-C-A-U-5MC-U.1: 15 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, K.69, E.72, R.88, Y.89 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.89 Hydrogen bonds: A:F.17, A:V.19, A:R.20 Water bridges: A:F.17, A:N.18 pi-Stacking: A:Y.89

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: E.58, T.59, K.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.59 Water bridges: A:E.58, A:T.59 SO4.3: 1 residues within 4Å: Chain A: R.52 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.52

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 P21212. To Be Published

Release Date

2022-06-22

Peptides

Y-box-binding protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Y-box-binding protein 2

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