Export Alignment
Secondary Structure
None DSSP PSIPRED SSpro
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
Use QMEANBrane values

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NGL PV

### Spike glycoprotein (S glycoprotein) | P0DTC2

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

Order by:

Oligo-State
  Homo-trimer
  (matching prediction)
GMQE
  0.73
QMEANDisCo Global:
  0.74 ± 0.05

Ligands
  2 x NAG, 2 x NAG-NAG, 1 x NAG-NAG-FUC, 6 x NAG-NAG-MAN
  2 x 2-acetamido-2-deoxy-beta-D-glucopyranose

  NAG.38: | 4 residues within 4Å: Chain A: G.339, N.343, L.368, S.371 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.368 Hydrogen bonds: A:S.371, A:S.371, A:S.371
  NAG.49: | 3 residues within 4Å: Chain B: K.147, N.149, M.153 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.147 Hydrogen bonds: B:N.149

  2 x 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

  NAG-NAG.6: | 4 residues within 4Å: Chain A: N.165, Chain C: Y.351, I.468, Ligand: NAG,NAG.6 No protein-ligand interaction detected (PLIP)
  NAG-NAG.26: | 4 residues within 4Å: Chain C: C.15, N.17, N.137, Ligand: NAG,NAG.26 No protein-ligand interaction detected (PLIP)

  1 x 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

  NAG-NAG-FUC.3: | 6 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074, Ligand: NAG,NAG,FUC.3, NAG,NAG,FUC.3 No protein-ligand interaction detected (PLIP)

  6 x alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

  NAG-NAG-MAN.4: | 8 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127, V.171, Ligand: NAG,NAG,MAN.4, NAG,NAG,MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171
  NAG-NAG-MAN.7: | 10 residues within 4Å: Chain A: T.108, N.234, T.236, Chain C: R.457, S.459, N.460, K.462, E.465, Ligand: NAG,NAG,MAN.7, NAG,NAG,MAN.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.236
  NAG-NAG-MAN.16: | 8 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, E.154, V.171, Ligand: NAG,NAG,MAN.16, NAG,NAG,MAN.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171
  NAG-NAG-MAN.19: | 10 residues within 4Å: Chain A: R.457, S.459, N.460, K.462, E.465, Chain B: T.108, N.234, T.236, Ligand: NAG,NAG,MAN.19, NAG,NAG,MAN.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.236
  NAG-NAG-MAN.28: | 10 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, E.154, E.169, V.171, Ligand: NAG,NAG,MAN.28, NAG,NAG,MAN.28 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171
  NAG-NAG-MAN.31: | 11 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462, E.465, Chain C: T.108, N.234, T.236, Ligand: NAG,NAG,MAN.31, NAG,NAG,MAN.31 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.236

QMEANDisCo Local
QMEAN Z-Scores

Template
6xr8.1.A Spike glycoprotein
Distinct conformational states of SARS-CoV-2 spike protein

Seq Identity
  100.00%
Coverage

Biounit Oligo State | Homo-trimer
QSQE | 0.85
Method | EM
Seq Similarity | 0.62
Coverage | 1.00
Range | 14-1162

Ligand | Added to Model | Description
--- | --- | ---
NAG | ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-FUC | ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-FUC | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-FUC | ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Not in contact with model. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Not in contact with model. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Not in contact with model. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Not in contact with model. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN | ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN-MAN | ✕ - Not in contact with model. | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN-MAN | ✕ - Not in contact with model. | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-MAN-MAN | ✕ - Not in contact with model. | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Model-Template Alignment

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