Structure of PDB 5spd Chain A

Receptor sequence
>5spdA (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence]
VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL
3D structure
PDB5spd Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
ChainA
Resolution1.05 Å
3D
structure
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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 QYJ A D22 G48 V49 A52 A129 G130 F156 L160 D20 G46 V47 A50 A127 G128 F154 L158
BS02 QYJ A D22 G48 V49 A52 G130 F156 D20 G46 V47 A50 G128 F154
BS03 QRU A D22 G48 V49 A52 L126 A129 G130 I131 F156 D20 G46 V47 A50 L124 A127 G128 I129 F154
External links
PDB RCSB:5spd, PDBe:5spd, PDBj:5spd
PDBsum5spd
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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