Structure of PDB 2amd Chain B

Receptor sequence

>2amdB (length=304)

GSSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAED
MLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKT
PKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSV
GFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDT
TITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVD
ILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVR
QCSG

3D structure

• PDB: 2amd Design of Wide-Spectrum Inhibitors Targeting Coronavirus Main Proteases.
• Chain: B
• Resolution: 1.85 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H41 G143 C145
• Catalytic site (residue number reindexed from 1): H43 G145 C147
• Enzyme Commision number: 2.1.1.-
  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	9IN	B	T26 N142 G143 C145 H163 H164 M165 E166 P168 R188 Q189 T190 A191	T28 N144 G145 C147 H165 H166 M167 E168 P170 R190 Q191 T192 A193	BindingDB: Ki=6700nM

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:2amd, PDBe:2amd, PDBj:2amd
• PDBsum: 2amd
• PubMed: 16128623
• UniProt: P0C6X7|R1AB_SARS Replicase polyprotein 1ab (Gene Name=rep)