7HCO: Non-structural protein 3

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000291. Determined by X-ray diffraction at 0.87 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 0.87 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 4,009
Mol. weight: 36.87 kDa
Ligands: A1A5X
Released: 11 Jun 2025

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

Secondary structure: helices and β-sheets

7HCO contains 26 α-helices and 14 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: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9	1
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	74-76	3
β-strand	80-84	5	1
β-strand	91-95	5	1
α-helix	100-102	3
α-helix	106-108	3
α-helix	109-114	6
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	158-167	10

Chain B: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9	1
β-strand	10-11	2	2
β-strand	16-20	5	2
α-helix	23-30	8
β-strand	34-38	5	2
α-helix	48-56	9
α-helix	60-72	13
α-helix	74-76	3
β-strand	80-84	5	2
β-strand	91-95	5	2
α-helix	100-102	3
α-helix	106-108	3
α-helix	109-114	6
α-helix	115-118	4
β-strand	121-124	4	2
α-helix	125-126	2
α-helix	130-132	3
α-helix	136-146	11
β-strand	150-155	6	2
α-helix	158-168	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 3	A, B	protein	169	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7HCO_1 Non-structural protein 3 (chains A, B)
SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNA
MQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHE
VLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFL

Ligands and cofactors

ID	Name	Formula	Copies
A1A5X	4-fluoro-3-({[1-(propan-2-yl)-1H-tetrazol-5-yl]sulfanyl}methyl)-1-benzothiophen…	C14 H13 F N4 O2 S2	1

Water and common crystallization additives (DMS) are not listed.

Primary citation

Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning. Correy, G.J., Rachman, M.M., Togo, T. et al. Sci Adv (2025) 11:eads7187-eads7187. DOI 10.1126/sciadv.ads7187 · 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)
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)

Browse structure collections

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