Structure of PDB 6yyt Chain A

Receptor sequence

>6yytA (length=853) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VYRAFDIYNDKVAGFAKFLKFSNYQHEETIYNLLKDCPAVARLTKYTMAD
LVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYA
NLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTT
PGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFT
EERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSF
GPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAA
DPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSK
GFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVV
DKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDA
LFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLL
KSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAM
PNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVK
PGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHR
LYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLV
ASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDY
VYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQE
YADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYT
PHT

3D structure

• PDB: 6yyt Structure of replicating SARS-CoV-2 polymerase.
• 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	C813 S814 R836 K849 R858	C737 S738 R760 K773 R782
BS02	rna	A	K500 S501 K545 V557 G559 R569 K577 G590 S592 S682 G683 D684 A685 Y915 F920	K424 S425 K469 V481 G483 R493 K501 G514 S516 S606 G607 D608 A609 Y839 F844
BS03	ZN	A	H295 C301 C306	H219 C225 C230
BS04	ZN	A	C487 H642 C645 C646	C411 H566 C569 C570

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:6yyt, PDBe:6yyt, PDBj:6yyt
• PDBsum: 6yyt
• PubMed: 32438371
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)