Structure of PDB 7l6r Chain A

Receptor sequence

>7l6rA (length=300) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SNSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYT
QLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDS
DLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEG
FFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVN
ASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMS
KFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

3D structure

• PDB: 7l6r Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16.
• Chain: A
• Resolution: 1.98 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	C6823 D6824 L6825 Y6828 S6831 A6832 L6834 M6840 N6841 K6844 D6873 K6874 Y6930 K6935 K6968 T6970 E6971 H6972 S6999 S7000	C27 D28 L29 Y32 S35 A36 L38 M44 N45 K48 D77 K78 Y134 K139 K172 T174 E175 H176 S203 S204
BS02	SAH	A	N6841 G6869 G6871 P6878 G6879 D6897 L6898 D6912 C6913 D6928 M6929 Y6930	N45 G73 G75 P82 G83 D101 L102 D116 C117 D132 M133 Y134
BS03	GLC	A	S6872 D6873 N6899 P6932	S76 D77 N103 P136
BS04	GLC	A	T6833 S7038 S7039 Y7040	T37 S242 S243 Y244
BS05	GLC	A	L6855 T6856 W6987	L59 T60 W191

Gene Ontology

Molecular Function

• GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity

External links

• PDB: RCSB:7l6r, PDBe:7l6r, PDBj:7l6r
• PDBsum: 7l6r
• PubMed: 34131072
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)