SMTL ID : 7qus.1

SARS-CoV-2 Spike, 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: 8 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, S.459, N.460, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain A: R.457, K.458, 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:K.458 NAG-NAG.6: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.7: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain B: R.457, S.459, N.460, K.462 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 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: 6 residues within 4Å: Chain A: N.164, N.165 Chain C: Y.351, L.452, T.470, F.490 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.470, A:N.164 NAG-FUC-NAG-FUC.8: 3 residues within 4Å: Chain A: Y.351 Chain B: N.164, N.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.164 NAG-FUC-NAG-FUC.12: 5 residues within 4Å: Chain B: Y.351, L.452, T.470 Chain C: N.164, N.165 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.470, C:N.164

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: 3 residues within 4Å: Chain A: N.122, N.125, V.127 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: 3 residues within 4Å: Chain A: G.339, N.343, S.371 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.616, T.618, 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: 3 residues within 4Å: Chain A: A.706, E.1072, 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.26: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.122, N.125, V.127 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: G.339, N.343, S.371 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.616, T.618, Q.644 Chain C: I.834 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: H.146, N.148, N.149 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.122, N.125, V.127 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: G.339, N.343, S.371 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain A: I.834 Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: H.146, N.148, N.149 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.25: 17 residues within 4Å: Chain A: R.408, Q.409, T.415, G.416 Chain B: C.336, P.337, F.338, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, L.513, F.515 17 PLIP interactions: 1 interactions with chain A, 16 interactions with chain B Salt bridges: A:R.408 Hydrophobic interactions: B:F.338, B:Y.365, B:Y.369, B:F.374, B:F.374, B:F.377, B:F.377, B:L.387, B:L.387, B:F.392, B:F.392, B:V.395, B:L.513, B:L.513, B:F.515, B:F.515 EIC.38: 16 residues within 4Å: Chain B: R.408, T.415, G.416 Chain C: C.336, P.337, F.338, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, L.513, F.515 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.338, C:Y.365, C:Y.369, C:F.374, C:F.374, C:F.377, C:F.377, C:L.387, C:L.387, C:F.392, C:F.392, C:V.395, C:L.513, C:L.513, C:F.515, C:F.515 Salt bridges: B:R.408 EIC.39: 15 residues within 4Å: Chain A: C.336, P.337, F.338, A.363, Y.365, Y.369, F.374, F.377, L.387, F.392, V.395, L.513, F.515 Chain C: R.408, T.415 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.338, A:Y.365, A:Y.369, A:F.374, A:F.374, A:F.377, A:F.377, A:L.387, A:L.387, A:F.392, A:F.392, A:V.395, A:L.513, A:L.513, A:F.515, A:F.515 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

2022-06-08

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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