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Secondary Structure
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Confidencegradient Confidenceclass Indels Chain Unique Chain Rainbow 2° Structure Clustal Hydrophobic Size Charged Polar Proline Ser/Thr Cysteine Aliphatic Aromatic No Colour
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NGL PV

### Proofreading exoribonuclease nsp14 (ExoN) | P0DTD1 PRO_0000449631

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

Order by:

Oligo-State
  Monomer
GMQE
  0.87
QMEANDisCo Global:
  0.82 ± 0.05

Ligands
  2 x ZN
  2 x ZINC ION

  ZN.1: | 5 residues within 4Å: Chain A: C.207, C.208, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.207, A:C.210, A:C.226, A:H.229
  ZN.2: | 4 residues within 4Å: Chain A: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.257, A:C.261, A:H.264, A:C.279

QMEANDisCo Local
QMEAN Z-Scores

Template
5nfy.1.A Polyprotein 1ab
SARS-CoV nsp10/nsp14 dynamic complex

Seq Identity
  94.88%
Coverage

Biounit Oligo State | Hetero-dimer
QSQE | 0.00
Method | X-ray, 3.38 Å
Seq Similarity | 0.62
Coverage | 1.00
Range | 3-525

Ligand | Added to Model | Description
--- | --- | ---
ZN | ✓ | ZINC ION
ZN | ✓ | ZINC ION
PEG | ✕ - Not biologically relevant. | DI(HYDROXYETHYL)ETHER
PEG | ✕ - Not in contact with model. | DI(HYDROXYETHYL)ETHER
ZN | ✕ - Clashing with protein. | ZINC ION
ZN | ✕ - Binding site not conserved. | ZINC ION
ZN | ✕ - Binding site not conserved. | ZINC ION

Model-Template Alignment

Oligo-State
  Monomer
GMQE
  0.86
QMEANDisCo Global:
  0.79 ± 0.05

Ligands
  1 x G3A, 1 x MG, 1 x SAH, 1 x ZN
  1 x GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE

  G3A.8: | 17 residues within 4Å: Chain B: N.306, C.309, R.310, Q.313, K.336, I.338, W.385, N.386, N.388, F.401, Y.420, N.422, K.423, F.426, T.428, F.506, Ligand: SAH.7 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.306, B:N.306, B:R.310, B:R.310, B:I.338, B:N.386, B:N.388, B:N.388 Salt bridges: B:R.310, B:R.310, B:R.310 pi-Stacking: B:W.385, B:F.426 pi-Cation interactions: B:R.310, B:R.310

  1 x MAGNESIUM ION

  MG.6: | 3 residues within 4Å: Chain B: D.90, A.187, E.191 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.90, B:E.191, B:E.191

  1 x S-ADENOSYL-L-HOMOCYSTEINE

  SAH.7: | 14 residues within 4Å: Chain B: W.292, G.333, N.334, P.335, D.352, A.353, Q.354, L.366, F.367, Y.368, W.385, N.386, C.387, V.389 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.353, B:Q.354, B:Y.368, B:Y.368, B:W.385

  1 x ZINC ION

  ZN.4: | 4 residues within 4Å: Chain B: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.257, B:C.261, B:H.264, B:C.279

QMEANDisCo Local
QMEAN Z-Scores

Template
5c8s.1.B Guanine-N7 methyltransferase
Crystal structure of the SARS coronavirus nsp14-nsp10 complex with functional ligands SAH and GpppA

Seq Identity
  95.07%
Coverage

Biounit Oligo State | Hetero-dimer
QSQE | 0.00
Method | X-ray, 3.33 Å
Seq Similarity | 0.62
Coverage | 1.00
Range | 1-525

Ligand | Added to Model | Description
--- | --- | ---
G3A | ✓ | GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
MG | ✓ | MAGNESIUM ION
SAH | ✓ | S-ADENOSYL-L-HOMOCYSTEINE
ZN | ✓ | ZINC ION
ZN | ✕ - Binding site not conserved. | ZINC ION
ZN | ✕ - Binding site not conserved. | ZINC ION
ZN | ✕ - Clashing with protein. | ZINC ION
ZN | ✕ - Clashing with protein. | ZINC ION

Model-Template Alignment

Oligo-State
  Monomer
GMQE
  0.85
QMEANDisCo Global:
  0.79 ± 0.05

Ligands
  1 x SAM, 2 x ZN
  1 x S-ADENOSYLMETHIONINE

  SAM.7: | 13 residues within 4Å: Chain B: W.292, G.333, P.335, D.352, A.353, Q.354, L.366, F.367, Y.368, W.385, N.386, C.387, V.389 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.386 Hydrogen bonds: B:G.333, B:A.353, B:Q.354, B:Y.368, B:Y.368, B:W.385 Salt bridges: B:R.310

  2 x ZINC ION

  ZN.3: | 4 residues within 4Å: Chain B: C.207, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.210, B:C.226, B:H.229, B:H.229
  ZN.4: | 4 residues within 4Å: Chain B: H.257, C.261, H.264, C.279 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.257, B:C.261, B:H.264

QMEANDisCo Local
QMEAN Z-Scores

Template
5c8t.1.B Guanine-N7 methyltransferase
Crystal structure of the SARS coronavirus nsp14-nsp10 complex with functional ligand SAM

Seq Identity
  95.07%
Coverage

Biounit Oligo State | Hetero-dimer
QSQE | 0.00
Method | X-ray, 3.20 Å
Seq Similarity | 0.62
Coverage | 1.00
Range | 1-525

Ligand | Added to Model | Description
--- | --- | ---
SAM | ✓ | S-ADENOSYLMETHIONINE
ZN | ✓ | ZINC ION
ZN | ✓ | ZINC ION
MG | ✕ - Not in contact with model. | MAGNESIUM ION
ZN | ✕ - Binding site not conserved. | ZINC ION
ZN | ✕ - Binding site not conserved. | ZINC ION
ZN | ✕ - Clashing with protein. | ZINC ION

Model-Template Alignment

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