Structure of PDB 8sqk Chain A

Receptor sequence

>8sqkA (length=929) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLK
TNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHD
FFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYN
CCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAG
IVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRA
LTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVN
CLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRE
LGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAA
LTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAI
SDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDK
SAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISA
KNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHN
MLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSH
RFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAV
TANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLR
KHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCW
TETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKT
DGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHML
DMYSVMLTNDNTSRYWEPEFYEAMYTPHT

3D structure

• PDB: 8sqk Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.
• Chain: A
• Resolution: 3.01 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 S814 R836 R858	S759 D760 S814 R836 R858
BS02	rna	A	K500 S501 N543 R569 G590 S592 S682 G683 A685 Y915 M924	K500 S501 N543 R569 G590 S592 S682 G683 A685 Y915 M924
BS03	rna	A	F35 I37 F48 L49 K50 N713	F35 I37 F48 L49 K50 N713
BS04	VSN	A	S682 D760	S682 D760
BS05	VSN	A	R33 F35 K50 R55 K73 R116 T120 K121 Y217 D218	R33 F35 K50 R55 K73 R116 T120 K121 Y217 D218
BS06	ZN	A	H295 C301	H295 C301
BS07	ZN	A	H642 C646	H642 C646
BS08	MG	A	N209 D218	N209 D218

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