Papain-like protease nsp3 | P0DTD1 PRO_0000449621

Structure
Assessment

Oligo-State: Monomer
(matching prediction)
GMQE: 0.14
QMEANDisCo Global:: 0.80 ± 0.05

Ligands

1 x ZN

QMEANDisCo Local

QMEAN Z-Scores

Template

6w9c.1.A Non-structural protein 3
The crystal structure of papain-like protease of SARS CoV-2

Seq Identity: 100.00%
Coverage

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: Monomer
GMQE: 0.14
QMEANDisCo Global:: 0.79 ± 0.05

Ligands

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

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

6wuu.2.A Non-structural protein 3
Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250

Seq Identity: 99.69%
Coverage

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: Monomer
GMQE: 0.14
QMEANDisCo Global:: 0.79 ± 0.05

Ligands

1 x TTT, 1 x ZN

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

3e9s.1.A Non-structural protein 3
A new class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

Seq Identity: 82.86%
Coverage

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

Model-Template Alignment

Structure
Assessment

Oligo-State: Monomer
GMQE: 0.14
QMEANDisCo Global:: 0.79 ± 0.05

Ligands

1 x TTT, 1 x ZN

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

3e9s.1.A Non-structural protein 3
A new class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

Seq Identity: 82.86%
Coverage

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

Model-Template Alignment

Structure
Assessment

Oligo-State: Monomer
GMQE: 0.14
QMEANDisCo Global:: 0.79 ± 0.05

Ligands

1 x TTT, 1 x ZN

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

7cmd.4.A Non-structural protein 3
Crystal structure of the SARS-CoV-2 PLpro with GRL0617

Seq Identity: 100.00%
Coverage

Ligand	Added to Model	Description
TTT	✓	5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide
ZN	✓	ZINC ION
ZN	✕ - Not in contact with model.	ZINC ION

Model-Template Alignment

Structure
Assessment

Oligo-State: Monomer
(matching prediction)
GMQE: 0.13
QMEANDisCo Global:: 0.79 ± 0.05

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

2w2g.1.A NON-STRUCTURAL PROTEIN 3
HUMAN SARS CORONAVIRUS UNIQUE DOMAIN

Seq Identity: 75.00%
Coverage

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

Model-Template Alignment

Structure
Assessment

Oligo-State: Monomer
GMQE: 0.09
QMEANDisCo Global:: 0.84 ± 0.07

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

6ywk.3.A NSP3 macrodomain
Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with HEPES

Seq Identity: 100.00%
Coverage

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-PIPERAZINE ETHANESULFONIC ACID
MG	✕ - Binding site not conserved.	MAGNESIUM ION

Model-Template Alignment

Structure
Assessment

Oligo-State: Monomer
GMQE: 0.07
QMEANDisCo Global:: 0.75 ± 0.07

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

2kqv.1.A 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

Seq Identity: 78.13%
Coverage

Model-Template Alignment

Structure
Assessment

Oligo-State: Monomer
GMQE: 0.05
QMEANDisCo Global:: 0.69 ± 0.08

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

2k87.1.A Non-structural protein 3 of Replicase polyprotein 1a
NMR STRUCTURE OF A PUTATIVE RNA BINDING PROTEIN (SARS1) FROM SARS CORONAVIRUS

Seq Identity: 81.74%
Coverage

Model-Template Alignment

Structure
Assessment

Oligo-State: Monomer
GMQE: 0.05
QMEANDisCo Global:: 0.71 ± 0.11

Ligands

QMEANDisCo Local

QMEAN Z-Scores

Template

2kqw.1.A 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

Seq Identity: 80.22%
Coverage

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 5, 2023 at 21:33

Model Results

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

Papain-like protease nsp3 | P0DTD1 PRO_0000449621

Created: May 5, 2023 at 21:33

Model Results

Background

Resolution