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NGL PV

### Papain-like protease nsp3 | P0DTD1 PRO_0000449621

### Created: May 5, 2023, 9:33 p.m. at 21:33

Order by:

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

Ligands
  1 x ZN
  1 x ZINC ION

  ZN.1: | 5 residues within 4Å: Chain A: C.934, T.936, C.937, C.969, C.971 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.934, A:C.937, A:C.969

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

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

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

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: 14 interactions with chain A Hydrophobic interactions: A:D.909, A:P.992, A:Y.1009 Hydrogen bonds: A:G.908, A:G.908, A:D.909, A:D.909, A:Y.1009, A:Y.1013, A:Y.1013, A:G.1016, A:G.1016, A:T.1046 Salt bridges: A:H.1017

  1 x ZINC ION

  ZN.2: | 4 residues within 4Å: Chain A: C.934, C.937, C.969, C.971 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.934, A:C.937, A:C.969, A:C.971

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

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

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

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: Chain A: L.907, G.908, D.909, P.992, P.993, Y.1009, Y.1013, Q.1014, Y.1018, T.1046 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.909, A:P.992, A:P.993, A:Y.1009, A:Y.1009, A:Y.1013, A:Q.1014, A:Q.1014, A:T.1046 Hydrogen bonds: A:D.909, A:D.909, A:Y.1013, A:Q.1014 pi-Stacking: A:Y.1013, A:Y.1013

  1 x ZINC ION

  ZN.2: | 4 residues within 4Å: Chain A: C.934, C.937, C.969, C.971 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.934, A:C.937, A:C.969, A:C.971

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

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

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

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: Chain A: L.907, G.908, D.909, P.992, P.993, Y.1009, Y.1013, Q.1014, Y.1018, T.1046 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.909, A:P.992, A:P.993, A:Y.1009, A:Y.1009, A:Y.1013, A:Q.1014, A:Q.1014, A:T.1046 Hydrogen bonds: A:D.909, A:D.909, A:Y.1013, A:Q.1014 pi-Stacking: A:Y.1013, A:Y.1013

  1 x ZINC ION

  ZN.2: | 4 residues within 4Å: Chain A: C.934, C.937, C.969, C.971 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.934, A:C.937, A:C.969, A:C.971

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

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

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

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: Chain A: L.907, G.908, D.909, M.953, P.992, P.993, Y.1009, G.1011, N.1012, Y.1013, Q.1014, Y.1018, T.1046 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.907, A:D.909, A:P.993, A:Y.1009, A:Y.1009, A:Y.1009, A:Q.1014, A:T.1046 Hydrogen bonds: A:D.909, A:Y.1013, A:Q.1014, A:Q.1014 pi-Stacking: A:Y.1013, A:Y.1013, A:Y.1013

  1 x ZINC ION

  ZN.2: | 5 residues within 4Å: Chain A: C.934, T.936, C.937, C.969, C.971 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.934, A:C.937

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

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

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

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

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

Model-Template Alignment

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

Biounit Oligo State | Monomer
QSQE | 0.00
Method | X-ray, 2.20 Å
Seq Similarity | 0.61
Coverage | 0.09
Range | 207-376

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

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

Biounit Oligo State | Monomer
QSQE | 0.00
Method | NMR
Seq Similarity | 0.55
Coverage | 0.10
Range | 551-675

Model-Template Alignment

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

Biounit Oligo State | Monomer
QSQE | 0.00
Method | NMR
Seq Similarity | 0.58
Coverage | 0.06
Range | 1089-1203

Model-Template Alignment

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

Biounit Oligo State | Monomer
QSQE | 0.00
Method | NMR
Seq Similarity | 0.55
Coverage | 0.09
Range | 678-732

Model-Template Alignment

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