8CB3: SARS-CoV Macro domain

SARS-CoV Macro domain complexed with 3-(N-morpholino)propanesulfonic acid. Determined by X-ray diffraction at 1.57 Å resolution. Released 7 Feb 2024.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Severe acute respiratory syndrome coronavirus
Chains: 3
Atoms: 4,464
Mol. weight: 56.21 kDa
Ligands: MPO
Released: 7 Feb 2024

Explore 8CB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CB3 contains 29 α-helices and 23 β-strands across 3 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	1
β-strand	17-21	5	1
α-helix	24-31	8
β-strand	35-39	5	1
α-helix	49-57	9
α-helix	61-73	13
β-strand	81-85	5	1
β-strand	92-96	5	1
α-helix	101-103	3
α-helix	109-115	7
α-helix	116-119	4
β-strand	122-125	4	1
α-helix	126-127	2
α-helix	131-133	3
α-helix	137-147	11
β-strand	151-156	6	1
β-strand	158	1	2
α-helix	159-172	14

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	3
β-strand	17-21	5	3
α-helix	24-31	8
β-strand	35-40	6	3
α-helix	49-57	9
α-helix	61-73	13
β-strand	81-85	5	3
β-strand	92-97	6	3
α-helix	101-103	3
α-helix	109-115	7
α-helix	116-119	4
β-strand	120	1	2
β-strand	122-125	4	3
α-helix	137-147	11
β-strand	151-156	6	3
α-helix	159-171	13

Chain C: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	4
β-strand	17-21	5	4
α-helix	24-31	8
β-strand	35-39	5	4
α-helix	49-57	9
α-helix	61-73	13
β-strand	81-85	5	4
β-strand	92-96	5	4
α-helix	101-103	3
α-helix	107-109	3
α-helix	110-115	6
α-helix	116-119	4
β-strand	122-125	4	4
α-helix	126-127	2
α-helix	131-133	3
α-helix	137-147	11
β-strand	151-156	6	4
α-helix	159-171	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Papain-like protease nsp3	A, B, C	protein	174	Severe acute respiratory syndrome coronavirus	P0C6X7 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8CB3_1 Papain-like protease nsp3 (chains A, B, C)
EEPVNQFTGYLKLTDNVAIKCVDIVKEAQSANPMVIVNAANIHLKHGGGVAGALNKATNG
AMQKESDDYIKLNGPLTVGGSCLLSGHNLAKKCLHVVGPNLNAGEDIQLLKAAYENFNSQ
DILLAPLLSAGIFGAKPLQSLQVCVQTVRTQVYIAVNDKALYEQVVMDYLDNLK

Ligands and cofactors

ID	Name	Formula	Copies
MPO	3[N-morpholino]propane sulfonic acid	C7 H15 N O4 S	1

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

Primary citation

Derivatives of MOPS: Promising scaffolds for SARS Coronaviruses macro domain-targeted inhibition. Ortega-Granda, O., Morin, B., Alvarez, K. et al. FEBS J (2025). DOI 10.1111/febs.70039

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…
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
8UFM 1.65 Å, Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SUD) from SARS-CoV-2
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…

Browse structure collections

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