9CY0: SARS-CoV-2 NSP3 macrodomain

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-4206. Determined by X-ray diffraction at 0.8 Å resolution. Released 12 Nov 2025.

Method: X-ray diffraction
Resolution: 0.8 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 6,183
Mol. weight: 37.31 kDa
Ligands: A1A55
Released: 12 Nov 2025

Explore 9CY0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CY0 contains 23 α-helices and 16 β-strands across 2 chains. 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	1
β-strand	16-20	5	1
α-helix	23-30	8
β-strand	34-38	5	1
α-helix	48-56	9
α-helix	60-72	13
α-helix	75-76	2
β-strand	80-84	5	1
β-strand	91-95	5	1
α-helix	100-102	3
β-strand	107	1	2
α-helix	108-114	7
α-helix	115-118	4
β-strand	121-124	4	1
α-helix	125-126	2
α-helix	130-132	3
α-helix	136-146	11
β-strand	150-155	6	1
α-helix	158-166	9

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9	1
β-strand	10-13	4	3
β-strand	16-19	4	3
α-helix	23-30	8
β-strand	34-38	5	3
α-helix	48-56	9
α-helix	60-72	13
α-helix	75-76	2
β-strand	80-84	5	3
β-strand	91-95	5	3
α-helix	100-102	3
β-strand	103	1	2
α-helix	108-114	7
α-helix	115-118	4
β-strand	121-124	4	3
α-helix	125-126	2
α-helix	130-132	3
α-helix	136-146	11
β-strand	150-154	5	3
α-helix	158-166	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Papain-like protease Non-structural protein 3	A, B	protein	170	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9CY0_1 Papain-like protease Non-structural protein 3 (chains A, B)
GEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNA
MQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHE
VLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLE

Ligands and cofactors

ID	Name	Formula	Copies
A1A55	N-{4-[(2,2-dimethyl-5-oxopyrrolidin-1-yl)amino]-9H-pyrimido[4,5-b]indol-8-yl}-N…	C19 H23 N7 O2	2

Primary citation

Ligand screen against SARS-CoV-2 NSP3 macrodomain. Correy, G.J., Fraser, J.S. To be published.

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)
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)
7TWR 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 8 (P43 crystal form)

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