- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 24 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)
NAG-NAG.1: 2 residues within 4Å:- Chain A: C.2, N.4
No protein-ligand interaction detected (PLIP)NAG-NAG.2: 5 residues within 4Å:- Chain A: N.109, T.111, N.112, V.114, V.158
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:V.158
NAG-NAG.3: 7 residues within 4Å:- Chain A: T.95, N.221, T.223
- Chain C: R.444, S.446, N.447, E.452
No protein-ligand interaction detected (PLIP)NAG-NAG.4: 2 residues within 4Å:- Chain A: N.603
- Chain B: I.821
No protein-ligand interaction detected (PLIP)NAG-NAG.5: 2 residues within 4Å:- Chain A: N.788, S.790
No protein-ligand interaction detected (PLIP)NAG-NAG.6: 3 residues within 4Å:- Chain A: N.704, L.909, Q.1058
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:L.909
NAG-NAG.7: 4 residues within 4Å:- Chain A: N.1085, T.1087, H.1088, F.1090
No protein-ligand interaction detected (PLIP)NAG-NAG.8: 1 residues within 4Å:- Chain A: N.1121
No protein-ligand interaction detected (PLIP)NAG-NAG.9: 2 residues within 4Å:- Chain B: N.330, S.358
No protein-ligand interaction detected (PLIP)NAG-NAG.10: 2 residues within 4Å:- Chain B: N.788, Q.791
No protein-ligand interaction detected (PLIP)NAG-NAG.11: 3 residues within 4Å:- Chain B: C.2, N.4, N.124
No protein-ligand interaction detected (PLIP)NAG-NAG.12: 5 residues within 4Å:- Chain B: N.109, T.111, N.112, V.114, V.158
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:V.158
NAG-NAG.13: 2 residues within 4Å:- Chain B: N.603
- Chain C: I.821
No protein-ligand interaction detected (PLIP)NAG-NAG.14: 1 residues within 4Å:- Chain B: N.1121
No protein-ligand interaction detected (PLIP)NAG-NAG.15: 4 residues within 4Å:- Chain B: N.1085, T.1087, H.1088, F.1090
No protein-ligand interaction detected (PLIP)NAG-NAG.16: 7 residues within 4Å:- Chain A: R.444, S.446, N.447, E.452
- Chain B: T.95, N.221, T.223
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.446, A:S.446
NAG-NAG.17: 3 residues within 4Å:- Chain B: N.704, L.909, Q.1058
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:L.909
NAG-NAG.18: 2 residues within 4Å:- Chain C: N.330, S.358
No protein-ligand interaction detected (PLIP)NAG-NAG.19: 2 residues within 4Å:- Chain A: I.821
- Chain C: N.603
No protein-ligand interaction detected (PLIP)NAG-NAG.20: 4 residues within 4Å:- Chain C: N.1085, T.1087, H.1088, F.1090
No protein-ligand interaction detected (PLIP)NAG-NAG.21: 3 residues within 4Å:- Chain C: N.704, L.909, Q.1058
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:L.909
NAG-NAG.22: 7 residues within 4Å:- Chain B: R.444, S.446, N.447, E.452
- Chain C: T.95, N.221, T.223
No protein-ligand interaction detected (PLIP)NAG-NAG.23: 5 residues within 4Å:- Chain C: N.109, T.111, N.112, V.114, V.158
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:V.158
NAG-NAG.24: 3 residues within 4Å:- Chain C: C.2, N.4, N.124
No protein-ligand interaction detected (PLIP)- 25 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)
NAG.25: 2 residues within 4Å:- Chain A: N.696, G.1118
Ligand excluded by PLIPNAG.26: 2 residues within 4Å:- Chain A: Y.15, N.48
Ligand excluded by PLIPNAG.27: 4 residues within 4Å:- Chain A: H.133, N.135, N.136, M.140
Ligand excluded by PLIPNAG.28: 3 residues within 4Å:- Chain A: N.152
- Chain C: Y.338, I.455
Ligand excluded by PLIPNAG.29: 3 residues within 4Å:- Chain A: N.267, E.268, N.269
Ligand excluded by PLIPNAG.30: 2 residues within 4Å:- Chain A: N.318, Q.567
Ligand excluded by PLIPNAG.31: 2 residues within 4Å:- Chain A: N.330, S.358
Ligand excluded by PLIPNAG.32: 2 residues within 4Å:- Chain A: S.698, N.1061
Ligand excluded by PLIPNAG.34: 2 residues within 4Å:- Chain B: Y.15, N.48
Ligand excluded by PLIPNAG.35: 3 residues within 4Å:- Chain B: H.133, N.135, N.136
Ligand excluded by PLIPNAG.36: 3 residues within 4Å:- Chain B: N.696, I.1117, G.1118
Ligand excluded by PLIPNAG.37: 4 residues within 4Å:- Chain A: Y.338, I.455
- Chain B: N.151, N.152
Ligand excluded by PLIPNAG.38: 3 residues within 4Å:- Chain B: A.693, E.1059, N.1061
Ligand excluded by PLIPNAG.39: 2 residues within 4Å:- Chain B: N.318, Q.567
Ligand excluded by PLIPNAG.40: 3 residues within 4Å:- Chain B: N.267, E.268, N.269
Ligand excluded by PLIPNAG.42: 2 residues within 4Å:- Chain C: Y.15, N.48
Ligand excluded by PLIPNAG.43: 3 residues within 4Å:- Chain C: N.696, I.1117, G.1118
Ligand excluded by PLIPNAG.44: 5 residues within 4Å:- Chain C: H.133, N.135, N.136, S.138, M.140
Ligand excluded by PLIPNAG.45: 4 residues within 4Å:- Chain C: N.788, S.790, Q.791
- Ligands: NAG.46
Ligand excluded by PLIPNAG.46: 1 residues within 4Å:- Ligands: NAG.45
Ligand excluded by PLIPNAG.47: 3 residues within 4Å:- Chain B: Y.338, I.455
- Chain C: N.152
Ligand excluded by PLIPNAG.48: 1 residues within 4Å:- Chain C: N.1121
Ligand excluded by PLIPNAG.49: 2 residues within 4Å:- Chain C: A.693, N.1061
Ligand excluded by PLIPNAG.50: 3 residues within 4Å:- Chain C: N.267, E.268, N.269
Ligand excluded by PLIPNAG.51: 2 residues within 4Å:- Chain C: N.318, Q.567
Ligand excluded by PLIP- 3 x STE: STEARIC ACID(Non-covalent)
STE.33: 20 residues within 4Å:- Chain A: R.395, Q.396, T.402, G.403
- Chain B: C.323, P.324, F.325, V.328, I.345, A.350, Y.352, L.355, F.361, F.364, L.374, F.379, V.382, I.421, L.500, F.502
22 PLIP interactions:18 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:F.325, B:F.325, B:V.328, B:I.345, B:A.350, B:Y.352, B:Y.352, B:L.355, B:F.361, B:F.364, B:F.364, B:L.374, B:F.379, B:F.379, B:V.382, B:I.421, B:L.500, B:F.502
- Water bridges: A:R.395, A:R.395, A:Q.396
- Salt bridges: A:R.395
STE.41: 20 residues within 4Å:- Chain B: R.395, Q.396, T.402, G.403
- Chain C: P.324, F.325, V.328, I.345, A.350, Y.352, L.355, Y.356, F.361, F.364, L.374, F.379, V.382, I.421, L.500, F.502
17 PLIP interactions:15 interactions with chain C, 2 interactions with chain B- Hydrophobic interactions: C:F.325, C:F.325, C:V.328, C:I.345, C:Y.352, C:L.355, C:Y.356, C:F.361, C:F.364, C:F.364, C:L.374, C:F.379, C:V.382, C:I.421, C:F.502
- Water bridges: B:Q.396
- Salt bridges: B:R.395
STE.52: 18 residues within 4Å:- Chain A: P.324, F.325, V.328, I.345, A.350, Y.352, F.361, F.364, L.374, F.379, V.382, I.421, L.500, F.502
- Chain C: R.395, Q.396, T.402, G.403
20 PLIP interactions:17 interactions with chain A, 3 interactions with chain C- Hydrophobic interactions: A:F.325, A:F.325, A:V.328, A:I.345, A:Y.352, A:Y.352, A:F.361, A:F.361, A:F.364, A:F.364, A:F.364, A:L.374, A:F.379, A:V.382, A:I.421, A:L.500, A:F.502
- Hydrogen bonds: C:Q.396, C:T.402
- Salt bridges: C:R.395
- 3 x R06: 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone(Covalent)
R06.53: 6 residues within 4Å:- Chain D: C.2, P.4, L.5, C.9, M.10, C.13
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:L.5
R06.54: 6 residues within 4Å:- Chain E: C.2, P.4, L.5, C.9, M.10, C.13
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:L.5
R06.55: 6 residues within 4Å:- Chain F: C.2, P.4, L.5, C.9, M.10, C.13
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:L.5
- 3 x KZ0: 2,4,6-tris(chloromethyl)-1,3,5-triazine(Covalent)
KZ0.56: 7 residues within 4Å:- Chain A: Y.436, S.481
- Chain G: C.2, P.3, T.10, C.11, C.14
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.436, A:Y.436
- pi-Stacking: A:Y.436
KZ0.57: 7 residues within 4Å:- Chain B: Y.436, S.481
- Chain H: C.2, P.3, T.10, C.11, C.14
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:Y.436
- pi-Stacking: B:Y.436
KZ0.58: 7 residues within 4Å:- Chain C: Y.436, S.481
- Chain I: C.2, P.3, T.10, C.11, C.14
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:Y.436, C:Y.436
- pi-Stacking: C:Y.436
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Pellegrino, S. et al., Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule. To Be Published
- Release Date
- 2025-03-26
- Peptides
- Spike glycoprotein: ABC
Biparatopic bicycle molecule (14mer): DEF
Biparatopic bicycle molecule (15mer): GHI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
I
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-3-3-3-mer
- Ligands
- 24 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)
- 25 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)
- 3 x STE: STEARIC ACID(Non-covalent)
- 3 x R06: 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone(Covalent)
- 3 x KZ0: 2,4,6-tris(chloromethyl)-1,3,5-triazine(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Pellegrino, S. et al., Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule. To Be Published
- Release Date
- 2025-03-26
- Peptides
- Spike glycoprotein: ABC
Biparatopic bicycle molecule (14mer): DEF
Biparatopic bicycle molecule (15mer): GHI - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
HI
I