SMTL ID : 5ytt.1

Crystal structure of YB1 cold-shock domain in complex with UCAUGU

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

U-C-A-U-G-U.1: 16 residues within 4Å: Chain A: K.17, W.18, N.20, R.22, N.23, G.24, Y.25, F.27, D.36, F.38, H.40, Q.41, K.71, G.72, A.73, E.74 Protein-ligand interaction information (PLIP) not available

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

SO4.2: 2 residues within 4Å: Chain A: R.54 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.54 SO4.3: 4 residues within 4Å: Chain A: K.45, K.46, R.54 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.46 Salt bridges: A:R.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X.J. et al., Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA. J.Biol.Chem. (2019)

Release Date

2018-12-05

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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