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Secondary Structure
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Colour Scheme
Fade Mismatches Enhance Mismatches
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

### nsp7 / nsp8 / Pol hetero-oligomeric complex | P0DTD1 PRO_0000449625, PRO_0000449626, PRO_0000449629

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

Order by:

Oligo-State
  Hetero-1-1-2-mer
GMQE
  0.74
QMEANDisCo Global:
  0.86 ± 0.05

Ligands
  2 x ZN
  2 x ZINC ION

  ZN.1: | 4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.295, A:C.301, A:C.306
  ZN.2: | 4 residues within 4Å: Chain A: C.487, H.642, C.645, C.646 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.487, A:C.645, A:C.646

QMEANDisCo Local
QMEAN Z-Scores

Template
6nur.1 NSP7, NSP12, NSP8

Seq Identity
  96.70%
Coverage

Biounit Oligo State | Hetero-tetramer
QSQE | -
Method | EM
Overall Seq Identity | 96.70%
Overall Seq Similarity | 0.61

Target | Seq Identity | Seq Similarity | Range | Coverage
--- | --- | --- | --- | ---
NSP7 | 98.80% | 0.59 | C: 2-71 | 1.00
NSP12 | 96.35% | 0.61 | A: 117-919 | 1.00
NSP8 | 97.47% | 0.59 | BD: 77-191 | 1.00

Ligand | Added to Model | Description
--- | --- | ---
ZN | ✓ | ZINC ION
ZN | ✓ | ZINC ION

Model-Template Alignment

Toggle Identical (BD)

Oligo-State
  Hetero-1-1-2-mer
GMQE
  0.72
QMEANDisCo Global:
  0.86 ± 0.05

Ligands
  1 x POP, 2 x ZN
  1 x PYROPHOSPHATE 2-

  POP.5: | 7 residues within 4Å: Chain A: K.50, N.52, K.73, R.116, N.209, Y.217, D.218 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.52, A:D.218, A:D.218 Salt bridges: A:K.50, A:K.50, A:K.73, A:K.73, A:R.116

  2 x ZINC ION

  ZN.1: | 4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.295, A:C.301, A:C.306, A:C.310
  ZN.2: | 5 residues within 4Å: Chain A: C.487, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.487, A:H.642, A:C.645, A:C.646

QMEANDisCo Local
QMEAN Z-Scores

Template
7aap.1 Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP

Seq Identity
  100.00%
Coverage

Biounit Oligo State | Hetero-tetramer
QSQE | 0.68
Method | EM
Overall Seq Identity | 100.00%
Overall Seq Similarity | 0.62

Target | Seq Identity | Seq Similarity | Range | Coverage
--- | --- | --- | --- | ---
Non-structural protein 7 | 100.00% | 0.59 | C: 2-68 | 1.00
Non-structural protein 12 | 100.00% | 0.63 | A: 4-929 | 1.00
Non-structural protein 8 | 100.00% | 0.60 | DB: 84-111 | 1.00

Ligand | Added to Model | Description
--- | --- | ---
POP | ✓ | PYROPHOSPHATE 2-
ZN | ✓ | ZINC ION
ZN | ✓ | ZINC ION
GE6 | ✕ - Binding site not conserved. | [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
MG | ✕ - Not in contact with model. | MAGNESIUM ION
MG | ✕ - Not in contact with model. | MAGNESIUM ION
MG | ✕ - Not in contact with model. | MAGNESIUM ION

Model-Template Alignment

Toggle Identical (DB)

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