SMTL ID : 7qur.1

SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, S.459, N.460, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain A: R.457, S.459, N.460, K.462, E.465 Chain B: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.459 NAG-NAG.6: 4 residues within 4Å: Chain B: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.922, B:N.925 NAG-NAG.7: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain B: R.457, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.922, C:N.925 NAG-NAG.11: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

3 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.4: 7 residues within 4Å: Chain A: N.164, N.165 Chain C: Y.351, A.352, L.452, T.470, F.490 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.470, C:T.470 NAG-FUC-NAG-FUC.8: 5 residues within 4Å: Chain A: Y.351, A.352, T.470 Chain B: N.164, N.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.470, A:T.470 NAG-FUC-NAG-FUC.12: 4 residues within 4Å: Chain B: Y.351, T.470 Chain C: N.164, N.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.470, B:T.470

36 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.13: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.122, T.124, N.125, E.154 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.616, Q.644 Chain B: I.834 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: H.146, N.148, N.149 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: C.15, N.17, N.137 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.122, T.124, N.125, E.154 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.616, Q.644 Chain C: I.834 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: H.146, N.148, N.149 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: N.122, T.124, N.125, E.154 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: G.339, N.343, L.368, S.371 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain A: I.834 Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: H.146, N.148, N.149 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP

3 x GE9: 2,3,5-tris(iodanyl)benzamide(Non-covalent)

GE9.25: 5 residues within 4Å: Chain A: Y.660, S.673, Q.675, I.693, Y.695 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.675 Hydrogen bonds: A:S.673 pi-Stacking: A:Y.660 GE9.40: 5 residues within 4Å: Chain B: Y.660, S.673, Q.675, I.693, Y.695 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.675 Hydrogen bonds: B:S.673 pi-Stacking: B:Y.660 GE9.56: 5 residues within 4Å: Chain C: Y.660, S.673, Q.675, I.693, Y.695 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.675 Hydrogen bonds: C:S.673 pi-Stacking: C:Y.660

3 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.26: 8 residues within 4Å: Chain A: Y.145, W.152, G.181, Q.183, H.245, S.247, L.249, T.259 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.152, A:H.245, A:T.259 Hydrogen bonds: A:Y.145, A:Q.183, A:S.247 SIA.41: 8 residues within 4Å: Chain B: Y.145, W.152, G.181, Q.183, H.245, S.247, L.249, T.259 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.152, B:H.245, B:T.259 Hydrogen bonds: B:Y.145, B:Q.183, B:S.247 SIA.57: 8 residues within 4Å: Chain C: Y.145, W.152, G.181, Q.183, H.245, S.247, L.249, T.259 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.152, C:H.245, C:T.259 Hydrogen bonds: C:Y.145, C:Q.183, C:S.247

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.27: 16 residues within 4Å: Chain A: R.408, Q.409, G.416 Chain B: P.337, F.338, V.341, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, L.513, F.515 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain B Water bridges: A:K.417 Salt bridges: A:R.408 Hydrophobic interactions: B:F.338, B:F.338, B:V.341, B:Y.365, B:Y.365, B:Y.369, B:F.374, B:F.374, B:F.377, B:F.377, B:L.387, B:F.392, B:F.392, B:L.513, B:F.515 EIC.42: 16 residues within 4Å: Chain B: R.408, Q.409, G.416 Chain C: P.337, F.338, V.341, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, L.513, F.515 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.338, C:F.338, C:V.341, C:Y.365, C:Y.365, C:Y.369, C:F.374, C:F.374, C:F.377, C:F.377, C:L.387, C:F.392, C:F.392, C:L.513, C:F.515 Water bridges: B:K.417 Salt bridges: B:R.408 EIC.43: 15 residues within 4Å: Chain A: P.337, F.338, V.341, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, L.513, F.515 Chain C: R.408, Q.409 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.338, A:F.338, A:V.341, A:Y.365, A:Y.365, A:Y.369, A:F.374, A:F.374, A:F.377, A:F.377, A:L.387, A:F.392, A:F.392, A:L.513, A:F.515 Hydrogen bonds: C:Q.409 Water bridges: C:K.417 Salt bridges: C:R.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buchanan, C.J. et al., Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science (2022)

Release Date

2022-06-01

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin

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