Structure of PDB 5smd Chain D

Receptor sequence

>5smdD (length=459) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

PTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMF
ITREEAIRHVRAWIGFDVEGCHGTNLPLQLGFSTGVNLVAVPTPLMYKGL
PWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTC
CLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNH
DLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINA
ACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCS
DKAYKIEELFYSYHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNL
NLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGIDY
VPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFD
TYNLWNTFT

3D structure

• PDB: 5smd PanDDA analysis group deposition
• Chain: D
• Resolution: 1.826 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	ZN	D	H257 C261 H264 C279	H200 C204 H207 C222
BS02	ZN	D	C452 C477 C484 H487	C393 C412 C419 H422
BS03	ZN	D	C207 C210 C226 H229	C150 C153 C169 H172
BS04	WKS	D	E92 H268 V269 D273	E69 H211 V212 D216

Gene Ontology

Molecular Function

• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
• GO:0004532 RNA exonuclease activity
• GO:0008168 methyltransferase activity

External links

• PDB: RCSB:5smd, PDBe:5smd, PDBj:5smd
• PDBsum: 5smd
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)