Structure of PDB 8sq9 Chain A

Receptor sequence

>8sq9A (length=926) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

AQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNC
CRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFK
FRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCD
DDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVG
VLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTA
ESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLD
DRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGV
VHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTN
NVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDY
DYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAG
FPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNR
ARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLK
TVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFY
RLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTAN
VNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHF
SMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTET
DLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGT
LMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMY
SVMLTNDNTSRYWEPEFYEAMYTPHT

3D structure

• PDB: 8sq9 Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.
• Chain: A
• Resolution: 2.9 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

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	S759 D760 C813 S814 R836 K849 E857 R858 S861 D865	S756 D757 C810 S811 R833 K846 E854 R855 S858 D862
BS02	rna	A	Q408 K500 S501 N507 Q541 N543 L544 V557 A558 R569 G590 S592 F594 S682 G683 D684 A685 Y689 Y915 M924	Q405 K497 S498 N504 Q538 N540 L541 V554 A555 R566 G587 S589 F591 S679 G680 D681 A682 Y686 Y912 M921
BS03	ZN	A	H295 C301 C306	H292 C298 C303
BS04	ZN	A	C487 H642 C645	C484 H639 C642
BS05	MG	A	D618 D760 D761	D615 D757 D758
BS06	MG	A	D618 Y619	D615 Y616
BS07	WSB	A	Y619 P620 D623 S682 T687 N691 D760	Y616 P617 D620 S679 T684 N688 D757
BS08	WSB	A	F35 I37 N39 F48 K50 N209 D218	F32 I34 N36 F45 K47 N206 D215

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:8sq9, PDBe:8sq9, PDBj:8sq9
• PDBsum: 8sq9
• PubMed: 37890482
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)