Structure of PDB 8gwm Chain A

Receptor sequence

>8gwmA (length=928) 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
SVMLTNDNTSRYWEPEFYEAMYTPHTVL

3D structure

• PDB: 8gwm A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors.
• Chain: A
• Resolution: 2.64 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 S814 R836 R858 D865	S756 S811 R833 R855 D862
BS02	rna	A	S501 N507 N543 V557 A558 S592 F594 S682 G683 D684 A685 Y915	S498 N504 N540 V554 A555 S589 F591 S679 G680 D681 A682 Y912
BS03	ZN	A	H295 C301 C306	H292 C298 C303
BS04	GNP	A	R33 F35 K50 R55 R116 T120 D208 N209 Y217 D218	R30 F32 K47 R52 R113 T117 D205 N206 Y214 D215
BS05	6GS	A	F35 I37 F48 L49 N713	F32 I34 F45 L46 N710

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:8gwm, PDBe:8gwm, PDBj:8gwm
• PDBsum: 8gwm
• PubMed: 36335936
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)