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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

### RNA-directed RNA polymerase nsp12 (Pol) | P0DTD1 PRO_0000449629

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

Order by:

Oligo-State
  Monomer
GMQE
  0.88
QMEANDisCo Global:
  0.87 ± 0.05

Ligands

QMEANDisCo Local
QMEAN Z-Scores

Template
6m71.1.A RNA-directed RNA polymerase
SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors

Seq Identity
  100.00%
Coverage

Biounit Oligo State | Hetero-tetramer
QSQE | 0.00
Method | EM
Seq Similarity | 0.63
Coverage | 1.00
Range | 31-932

Model-Template Alignment

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

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

  POP.3: | 3 residues within 4Å: Chain A: R.553, C.622, D.623 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.553, A:C.622, A:D.623, A:D.623

  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
7bv2.1.A RNA-directed RNA polymerase
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)

Seq Identity
  100.00%
Coverage

Biounit Oligo State | Hetero-trimer
QSQE | 0.00
Method | EM
Seq Similarity | 0.63
Coverage | 1.00
Range | 31-929

Ligand | Added to Model | Description
--- | --- | ---
POP | ✓ | PYROPHOSPHATE 2-
ZN | ✓ | ZINC ION
ZN | ✓ | ZINC ION
F86 | ✕ - Binding site not conserved. | [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate
MG | ✕ - Not in contact with model. | MAGNESIUM ION
MG | ✕ - Binding site not conserved. | MAGNESIUM ION

Model-Template Alignment

Oligo-State
  Monomer
GMQE
  0.85
QMEANDisCo Global:
  0.89 ± 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.A NSP12
SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors

Seq Identity
  96.35%
Coverage

Biounit Oligo State | Hetero-tetramer
QSQE | 0.00
Method | EM
Seq Similarity | 0.61
Coverage | 1.00
Range | 117-919

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

Model-Template Alignment

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