Structure of PDB 7b3b Chain A

Receptor sequence

>7b3bA (length=814) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VYRAFDIYNDKVAGFAKFLKRLTKYTMADLVYALRHFDEGNCDTLKEILV
TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMR
NAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTL
TRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPN
CVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYH
FRELGVVHNQDVNLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALT
NNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISD
YDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSA
GFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKN
RARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNML
KTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRF
YRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTA
NVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKH
FSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTE
TDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDG
TLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTDNTSRY
WEPEFYEAMYTPHT

3D structure

• PDB: 7b3b Mechanism of SARS-CoV-2 polymerase stalling by remdesivir.
• Chain: A
• Resolution: 3.1 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	D760 C813 S814 R836 R858 S861 D865	D658 C711 S712 R734 R756 S759 D763
BS02	rna	A	N496 K500 S501 N543 K545 A558 G559 R569 K577 G590 S592 F594 Y595 S682 G683 D684 A685 Y689 Y915 M924	N394 K398 S399 N441 K443 A456 G457 R467 K475 G488 S490 F492 Y493 S580 G581 D582 A583 Y587 Y800 M809
BS03	ZN	A	H295 C301 C306	H198 C204 C209
BS04	ZN	A	C487 H642 C645 C646	C385 H540 C543 C544

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:7b3b, PDBe:7b3b, PDBj:7b3b
• PDBsum: 7b3b
• PubMed: 33436624
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)