Papain-like protease nsp3 | P0DTD1 PRO_0000449621

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Monomer (matching prediction)

1 x ZN

0.14

0.80 ± 0.05

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
6w9c.1.A	100.00%		Non-structural protein 3 The crystal structure of papain-like protease of SARS CoV-2

Ligand	Added to Model	Description
ZN	✓	ZINC ION
CL	✕ - Not biologically relevant.	CHLORIDE ION
CL	✕ - Not biologically relevant.	CHLORIDE ION
CL	✕ - Not biologically relevant.	CHLORIDE ION
ZN	✕ - Binding site not conserved.	ZINC ION
ZN	✕ - Binding site not conserved.	ZINC ION
ZN	✕ - Binding site not conserved.	ZINC ION

Model-Template Alignment

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Monomer

1 x ACE-UB4-DPP-GLY-GVE, 1 x ZN

0.14

0.79 ± 0.05

1 x VIR250

ACE-UB4-DPP-GLY-GVE.1:

22 residues within 4Å:

Chain A: W.851, N.854, C.856, Y.857, L.907, G.908, D.909, R.911, M.953, P.992, Y.1009, Y.1013, Q.1014, C.1015, G.1016, H.1017, Y.1018, T.1046,
Ligand: ACE,UB4,DPP,GLY,GVE.1, ACE,UB4,DPP,GLY,GVE.1, ACE,UB4,DPP,GLY,GVE.1, ACE,UB4,DPP,GLY,GVE.1

14 PLIP interactions:

1 x ZINC ION

ZN.2:

4 residues within 4Å:

4 PLIP interactions:

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
6wuu.2.A	99.69%		Non-structural protein 3 Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250

Ligand	Added to Model	Description
ACE-UB4-DPP-GLY-GVE	✓	VIR250
ZN	✓	ZINC ION
MG	✕ - Not in contact with model.	MAGNESIUM ION

Model-Template Alignment

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Monomer

1 x TTT, 1 x ZN

0.14

0.80 ± 0.05

1 x 5-AMINO-2-METHYL-N-[(1R)-1-NAPHTHALEN-1-YLETHYL]BENZAMIDE

TTT.1:

10 residues within 4Å:

15 PLIP interactions:

1 x ZINC ION

ZN.2:

4 residues within 4Å:

4 PLIP interactions:

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
3e9s.1.A	82.86%		Non-structural protein 3 A new class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

Ligand	Added to Model	Description
TTT	✓	5-AMINO-2-METHYL-N-[(1R)-1-NA…
ZN	✓	ZINC ION
CL	✕ - Not biologically relevant.	CHLORIDE ION
CL	✕ - Not biologically relevant.	CHLORIDE ION

Model-Template Alignment

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Monomer

1 x TTT, 1 x ZN

0.14

0.80 ± 0.05

1 x 5-AMINO-2-METHYL-N-[(1R)-1-NAPHTHALEN-1-YLETHYL]BENZAMIDE

TTT.1:

10 residues within 4Å:

15 PLIP interactions:

1 x ZINC ION

ZN.2:

4 residues within 4Å:

4 PLIP interactions:

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
3e9s.1.A	82.86%		Non-structural protein 3 A new class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

Ligand	Added to Model	Description
TTT	✓	5-AMINO-2-METHYL-N-[(1R)-1-NA…
ZN	✓	ZINC ION
CL	✕ - Not biologically relevant.	CHLORIDE ION
CL	✕ - Not biologically relevant.	CHLORIDE ION

Model-Template Alignment

Structure
Assessment

Oligo-State

Ligands

GMQE

QMEANDisCo Global

Monomer

1 x TTT, 1 x ZN

0.14

0.79 ± 0.05

1 x 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide

TTT.1:

13 residues within 4Å:

15 PLIP interactions:

1 x ZINC ION

ZN.2:

5 residues within 4Å:

2 PLIP interactions:

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
7cmd.4.A	100.00%		Non-structural protein 3 Crystal structure of the SARS-CoV-2 PLpro with GRL0617

Model-Template Alignment

Structure
Assessment

Oligo-State	Ligands	GMQE	QMEANDisCo Global
Monomer (matching prediction)	None	0.13	0.79 ± 0.05

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
2w2g.1.A	75.00%		NON-STRUCTURAL PROTEIN 3 HUMAN SARS CORONAVIRUS UNIQUE DOMAIN

Model-Template Alignment

Structure
Assessment

Oligo-State	Ligands	GMQE	QMEANDisCo Global
Monomer	None	0.09	0.84 ± 0.07

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
6ywk.3.A	100.00%		NSP3 macrodomain Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with HEPES

Model-Template Alignment

Structure
Assessment

Oligo-State	Ligands	GMQE	QMEANDisCo Global
Monomer	None	0.07	0.76 ± 0.07

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
2kqv.1.A	78.13%		Non-structural protein 3 SARS coronavirus-unique domain (SUD): Three-domain molecular architecture in solution and RNA binding. I: Structure of the SUD-M domain of SUD-MC

Model-Template Alignment

Structure
Assessment

Oligo-State	Ligands	GMQE	QMEANDisCo Global
Monomer	None	0.05	0.69 ± 0.08

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
2k87.1.A	81.74%		Non-structural protein 3 of Replicase polyprotein 1a NMR STRUCTURE OF A PUTATIVE RNA BINDING PROTEIN (SARS1) FROM SARS CORONAVIRUS

Model-Template Alignment

Structure
Assessment

Oligo-State	Ligands	GMQE	QMEANDisCo Global
Monomer	None	0.05	0.71 ± 0.11

QMEANDisCo Local

QMEAN Z-Scores

Template	Seq Identity	Coverage	Description
2kqw.1.A	80.22%		Non-structural protein 3 SARS coronavirus-unique domain (SUD): Three-domain molecular architecture in solution and RNA binding. II: Structure of the SUD-C domain of SUD-MC

Model-Template Alignment

Biounit Oligo State	Homo-trimer
QSQE	0.26
Method	X-ray, 2.70 Å
Seq Similarity	0.63
Coverage	0.16
Range	748-1060

Biounit Oligo State	Monomer
QSQE	0.00
Method	X-ray, 2.79 Å
Seq Similarity	0.62
Coverage	0.16
Range	744-1061

Biounit Oligo State	Monomer
QSQE	0.00
Method	X-ray, 2.50 Å
Seq Similarity	0.57
Coverage	0.16
Range	746-1059

Biounit Oligo State	Monomer
QSQE	0.00
Method	X-ray, 2.50 Å
Seq Similarity	0.57
Coverage	0.16
Range	746-1059

Biounit Oligo State	Monomer
QSQE	0.00
Method	X-ray, 2.59 Å
Seq Similarity	0.63
Coverage	0.16
Range	746-1060

Papain-like protease nsp3 | P0DTD1 PRO_0000449621

Created: May 18, 2022 at 17:42

Model Results

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Click model image to view in 3D

Biounit Oligo State	Homo-dimer
QSQE	0.21
Method	X-ray, 2.22 Å
Seq Similarity	0.53
Coverage	0.14
Range	413-676

Ligand	Added to Model	Description
SO4	✕ - Not biologically relevant.	SULFATE ION
SO4	✕ - Not biologically relevant.	SULFATE ION

Ligand	Added to Model	Description
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EDO	✕ - Not biologically relevant.	1,2-ETHANEDIOL
EPE	✕ - Not biologically relevant.	4-(2-HYDROXYETHYL)-1-PIPERAZI…
MG	✕ - Binding site not conserved.	MAGNESIUM ION

Papain-like protease nsp3 | P0DTD1 PRO_0000449621

Created: May 18, 2022 at 17:42

Model Results

Background

Resolution

Click model image to view in 3D

Click model image to view in 3D