Structure of PDB 1yvp Chain A Binding Site BS01

Receptor Information

>1yvp Chain A (length=529) Species: 8355 (Xenopus laevis)

MDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLG
QENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSD
IKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSD
WYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSK
GWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLV
REHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSV
CERLTNEKLLKKARIHPFHILVALETYKKGHGLRWIPDTSIVEALDNAFY
KSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEK
DSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTN
TAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSI
ADPDDRGMLDICGFDSGALDVIRNFTLDL

Ligand information

>1yvp Chain C (length=10)

gcugguccga

..........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1yvp Structural Insights into RNA Quality Control: The Ro Autoantigen Binds Misfolded RNAs via Its Central Cavity
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): K108 Q109 K133 G142 W144 G145 R146 A147 R149 W177 D181 R184 L185 H187
• Binding residue (residue number reindexed from 1): K104 Q105 K129 G138 W140 G141 R142 A143 R145 W173 D177 R180 L181 H183
• Binding affinity: PDBbind-CN: Kd=5.2nM

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0034336 misfolded RNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0030030 cell projection organization

Cellular Component

• GO:0005737 cytoplasm
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:1yvp, PDBe:1yvp, PDBj:1yvp
• PDBsum: 1yvp
• PubMed: 15907467
• UniProt: P42700|RO60_XENLA RNA-binding protein RO60 (Gene Name=ro60)