Structure of PDB 7krn Chain A

Receptor sequence

>7krnA (length=927) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

DAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTN
CCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFF
KFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCC
DDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIV
GVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALT
AESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCL
DDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELG
VVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALT
NNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISD
YDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSA
GFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKN
RARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNML
KTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRF
YRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTA
NVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKH
FSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTE
TDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDG
TLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDM
YSVMLTNDNTSRYWEPEFYEAMYTPHT

3D structure

• PDB: 7krn Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.
• Chain: A
• Resolution: 3.4 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	K551 R553 R555 C813 S814 R836 K849 R858 S861 D865	K549 R551 R553 C811 S812 R834 K847 R856 S859 D863
BS02	rna	A	N496 K500 S501 V557 K577 G590 S592 F594 Y595 S682 G683 D684 A685 Y689 Y915	N494 K498 S499 V555 K575 G588 S590 F592 Y593 S680 G681 D682 A683 Y687 Y913
BS03	ZN	A	H295 C301 C306	H293 C299 C304
BS04	ZN	A	C487 H642 C646	C485 H640 C644
BS05	MG	A	N209 D218	N207 D216
BS06	ADP	A	N52 H75 R116 Y217 D218	N50 H73 R114 Y215 D216
BS07	1N7	A	V204 D221 I223	V202 D219 I221
BS08	1N7	A	R197 V231 Y289	R195 V229 Y287
BS09	1N7	A	S904 V905	S902 V903

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:7krn, PDBe:7krn, PDBj:7krn
• PDBsum: 7krn
• PubMed: 33883267
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)