8UFM: Papain-like protease nsp3

Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SUD) from SARS-CoV-2. Determined by X-ray diffraction at 1.65 Å resolution. Released 18 Oct 2023.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 1
Atoms: 2,209
Mol. weight: 30.54 kDa
Released: 18 Oct 2023

Explore 8UFM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UFM contains 17 α-helices and 16 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	417-420	4	1
α-helix	425-428	4
β-strand	435-439	5	1
α-helix	444	1
β-strand	445	1	1
α-helix	446	1
α-helix	447-450	4
α-helix	459-463	5
β-strand	472-475	4	1
β-strand	478-482	5	1
α-helix	492-499	8
α-helix	503	1
β-strand	506-509	4	1
α-helix	515-517	3
α-helix	521-529	9
β-strand	534-537	4	1
α-helix	538-539	2
α-helix	550-552	3
β-strand	553	1	2
α-helix	557-567	11
β-strand	570-574	5	3
α-helix	578-587	10
β-strand	596-600	5	3
β-strand	602-607	6	3
α-helix	613-623	11
β-strand	627-629	3	3
α-helix	630-631	2
β-strand	634	1	4
β-strand	639	1	4
α-helix	641-648	8
β-strand	655-657	3	3
β-strand	658	1	2
α-helix	662-670	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Papain-like protease nsp3	A	protein	269	Severe acute respiratory syndrome coronavirus 2	P0C6X7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8UFM_1 Papain-like protease nsp3 (chains A)
SNAKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIV
GDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGCNGYTVEEAKTVLK
KCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYK
GIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARCMR
SLKVPATVSVSSPDAVTAYNGYLTSSSKT

Primary citation

Torsional twist of the SARS-CoV and SARS-CoV-2 SUD-N and SUD-M domains. Rosas-Lemus, M., Minasov, G., Brunzelle, J.S. et al. Protein Sci (2025) 34:e70050-e70050. DOI 10.1002/pro.70050 · PubMed

Other PDB entries of the same protein (UniProt P0C6X7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ACF 1.4 Å, NMR structure of SARS-CoV non-structural protein NSP3A (SARS1) from SARS coronavirus
6W79 1.46 Å, Structure of SARS-CoV main protease bound to potent broad-spectrum non-covalent…
6WCO 1.48 Å, Structure of SARS main protease bound to inhibitor X47
5C5O 1.5 Å, Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type…
8CB3 1.57 Å, SARS-CoV Macro domain complexed with 3-(N-morpholino)propanesulfonic acid
3TNT 1.59 Å, Crystal structure of SARS coronavirus main protease complexed with an alpha,…
4TWY 1.6 Å, Structure of SARS-3CL protease complex with a phenylbenzoyl (S,R)-N-decalin type inhibitor
7FA1 1.6 Å, Crystal Structure of N-terminus of the non-structural protein 2 from SARS coronavirus
5N19 1.62 Å, Structure of SARS coronavirus main protease in complex with the alpha-ketoamide…
2ZU5 1.65 Å, complex structure of SARS-CoV 3CL protease with TG-0205486
3SZN 1.69 Å, Crystal structure of SARS coronavirus main protease complexed with an alpha,…
5C5N 1.69 Å, Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (R,S)-N-decalin type…

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