Structure of PDB 7qdy Chain A

Receptor sequence

>7qdyA (length=1169) Species: 9606 (Homo sapiens)

MMETERLVLPPPDPLDLPLRAVELGCTGHWELLNLPGAPESSLPHGLPPC
APDLQQEAEQLFLSSPAWLPLHGVEHSARKWQRKTDPWSLLAVLGAPVPS
DLQAQRHPTTGQILGYKEVLLENTNLSATTSLSLRRPPGPASQSLWGNPT
QYPFWPGGMDEPTITDLNTREEAEEEIDFEKDLLTIPPGFKKGMDFAPKD
CAPGLLLARASSLEDLVLKEQWAIPVDATSPVGDFYRLIPQPAFQWAFEP
DVFQKQAILHLERHDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSP
IKALSNQKFRDFRNTFGDVGLLTGDVQLHPEASCLIMTTEILRSMLYSGS
DVIRDLEWVIFDEVHYINDVERGVVWEEVLIMLPDHVSIILLSATVPNAL
EFADWIGRLKRRQIYVISTVTRPVPLEHYLFTGNSSKTQGELFLLLDSRG
AFHTKGYYAAVEAKKERMGPAQDRGVYLSLLASLRTRAQLPVVVFTFSRG
RCDEQASGLTSLDLTTSSEKSEIHLFLQRCLARLRGSDRQLPQVLHMSEL
LNRGLGVHHSGILPILKEIVEMLFSRGLVKVLFATETFAMGVNMPARTVV
FDSMRKHDGSTFRDLLPGEYVQMAGRAGRRGLDPTGTVILLCKGRVPEMA
DLHRMMMGKPSQLQSQFRLTYTMILNLLRVDALRVEDMMKRSFSEFPSRK
DSKAHEQALAELTKRLGALEEPDMTGQLVDLPEYYSWGEELTETQHMIQR
RIMESVNGLKSLSAGRVVVVKNQEHHNALGVILQVSSNSTSRVFTTLVLC
DKPLSQDPQDRGPATAEVPYPDDLVGFKLFLPEGPCDHTVVKLQPGDMAA
ITTKVLRVNGEKILEDFSKRQQPKFKKDPPLAAVTTAVQELLRLAQAHPA
GPPTLDPVNDLQLKDMSVVEGGLRARKLEELIQGAQCVHSPRFPAQYLKL
RERMQIQKEMERLRFLLSDQSLLLLPEYHQRVEVLRTLGYVDEAGTVKLA
GRVACAMSSHELLLTELMFDNALSTLRPEEIAALLSGLVCQSPGDAGDQL
PNTLKQGIERVRAVAKRIGEVQVACGLNQTVEEFVGELNFGLVEVVYEWA
RGMPFSELAGLSGTPEGLVVRCIQRLAEMCRSLRGAARLVGEPVLGAKME
TAATLLRRDIVFAASLYTQ

3D structure

• PDB: 7qdy The human SKI complex regulates channeling of ribosome-bound RNA to the exosome via an intrinsic gatekeeping mechanism.
• Chain: A
• Resolution: 3.1 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	K363 G385 E401 R433 F574 S575 R576 S637 E663 T664 M667 H684 D685 S1085 Q1118 R1198	K302 G324 E340 R372 F497 S498 R499 S560 E586 T587 M590 H607 D608 S1008 Q1041 R1121

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0034458 3'-5' RNA helicase activity

Biological Process

• GO:0006401 RNA catabolic process
• GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay
• GO:0072344 rescue of stalled ribosome

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0055087 Ski complex

External links

• PDB: RCSB:7qdy, PDBe:7qdy, PDBj:7qdy
• PDBsum: 7qdy
• PubMed: 35120588
• UniProt: Q15477|SKI2_HUMAN Superkiller complex protein 2 (Gene Name=SKIC2)