7SI9: 3C-like proteinase

Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with PF-07321332. Determined by X-ray diffraction at 2.0 Å resolution. Released 20 Oct 2021.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 1
Atoms: 2,537
Mol. weight: 34.33 kDa
Ligands: 4WI
Released: 20 Oct 2021

Explore 7SI9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SI9 contains 15 α-helices and 19 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: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-14	4
β-strand	17-22	6	1
β-strand	25-32	8	1
β-strand	35-39	5	1
α-helix	40-43	4
α-helix	54-59	6
α-helix	63-65	3
β-strand	66-70	5	1
β-strand	73-75	3	1
α-helix	76	1
β-strand	77-83	7	1
β-strand	86-91	6	1
α-helix	98-99	2
β-strand	101-103	3	2
β-strand	111-118	8	2
β-strand	121-129	9	2
β-strand	136	1	2
β-strand	148-153	6	2
β-strand	156-166	11	2
β-strand	172-175	4	2
α-helix	180	1
β-strand	181	1	2
β-strand	199	1	3
α-helix	201-213	13
α-helix	227-236	10
β-strand	239	1	3
α-helix	240-242	3
α-helix	244-249	6
α-helix	251-257	7
α-helix	261-274	14
β-strand	281	1	4
β-strand	284	1	4
α-helix	293-301	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3C-like proteinase	A	protein	306	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7SI9_1 3C-like proteinase (chains A)
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR
KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG
SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN
FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligands and cofactors

ID	Name	Formula	Copies
4WI	(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dim…	C23 H34 F3 N5 O4	1

Primary citation

Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease. Kneller, D.W., Li, H., Phillips, G. et al. Nat Commun (2022) 13:2268. DOI 10.1038/s41467-022-29915-z · PubMed

Other PDB entries of the same protein (UniProt P0DTD1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

44PS 0.77 Å, 6-conformation model of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
7KR0 0.77 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
9CY0 0.8 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-4206
7TX0 0.84 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43…
7KQO 0.85 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (P43 crystal form)
7HCO 0.87 Å, PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in…
7KQP 0.88 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal…
7TWJ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 4 (P43 crystal form)
7TWN 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 5 (P43 crystal form)
7TWO 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 6 (P43 crystal form)
7TWP 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 7 (P43 crystal form)
7TWQ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 9 (P43 crystal form)

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