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Spike glycoprotein (S glycoprotein) | P0DTC2
Created: May 5, 2023 at 21:33
Model 01
- 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-glucopyranoseNAG.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-glucopyranoseNAG-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-glucopyranoseNAG-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-glucopyranoseNAG-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
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 |
|---|---|---|
| ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✓ | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Not in contact with model. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - 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 | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - 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 | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - 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 | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - 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 | |
| ✕ - Clashing with protein. | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
| ✕ - 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 | |
| ✕ - 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 | |
| ✕ - 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 |
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