Structure of PDB 7dfg Chain A

Receptor sequence

>7dfgA (length=908) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

QSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCC
RFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKF
RIDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDY
FNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLT
LDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESH
VDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRC
ILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHN
QDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVA
FQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYY
RYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPF
NKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRART
VAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVY
SDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLA
NECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNA
LLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMM
ILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLT
KGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMI
ERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTTSRYWEPEFY
EAMYTPHT

3D structure

• PDB: 7dfg Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
• Chain: A
• Resolution: 2.7 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 C813 S814 R836 K849 R858 S861 D865	S753 C807 S808 R830 K843 R852 S855 D859
BS02	rna	A	K500 S501 N507 N543 V557 K577 G590 S592 F594 Y595 S682 G683 D684 A685 Y689 Y915 F920 M924	K494 S495 N501 N537 V551 K571 G584 S586 F588 Y589 S676 G677 D678 A679 Y683 Y894 F899 M903
BS03	1RP	A	D623 S682 D760	D617 S676 D754
BS04	ZN	A	H295 C301 C306 C310	H289 C295 C300 C304
BS05	ZN	A	C487 H642 C645 C646	C481 H636 C639 C640
BS06	MG	A	D760 D761	D754 D755
BS07	POP	A	K50 K73 R116 D218	K46 K69 R110 D212
BS08	MG	A	N209 D218	N203 D212

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