SMTL ID : 9b0y.1

SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x 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-FUC.1: 6 residues within 4Å: Chain C: S.743, A.745, S.750, E.1111, K.1112, N.1113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1113 Hydrophobic interactions: C:A.745 NAG-NAG-FUC.9: 6 residues within 4Å: Chain A: S.743, A.745, S.750, E.1111, K.1112, N.1113 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.745 NAG-NAG-FUC.16: 6 residues within 4Å: Chain B: A.745, S.750, N.1113, F.1114, T.1115 Chain C: Q.934 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 5 residues within 4Å: Chain A: N.748, N.749, I.1169, G.1170 Chain B: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: T.147, T.148, N.273, T.275 Chain C: K.497, K.501 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: N.748, N.749, I.1169, G.1170 Chain C: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain A: D.835 Chain C: N.748, N.749, I.1169, G.1170 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain A: A.885, R.886 Chain C: N.655, T.657, E.658 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.840, S.842, Q.843, Q.974 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain A: N.319, E.320, N.321, T.325 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain A: N.1137, G.1138, T.1139, H.1140, F.1142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1140 NAG-NAG-BMA.8: 5 residues within 4Å: Chain A: C.1121, C.1165, D.1166, I.1171, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain B: N.319, E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain B: N.756, T.758, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.961 NAG-NAG-BMA.17: 9 residues within 4Å: Chain A: F.495, N.526, Y.528 Chain B: F.381, N.382, V.406, L.407, S.410, F.413 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.410, A:Y.528 NAG-NAG-BMA.18: 4 residues within 4Å: Chain C: N.319, E.320, N.321, T.325 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 5 residues within 4Å: Chain C: N.1137, G.1138, T.1139, H.1140, F.1142 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1140 NAG-NAG-BMA.21: 2 residues within 4Å: Chain C: D.1166, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 6 residues within 4Å: Chain C: N.756, T.758, L.961, N.964, Q.965, Q.1110 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.961, C:N.964, C:Q.965 NAG-NAG-BMA.25: 7 residues within 4Å: Chain B: F.495, G.524, F.525, Y.528 Chain C: G.378, N.382, V.406 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.528, B:Y.528

5 x 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.6: 7 residues within 4Å: Chain A: N.756, F.757, T.758, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.961 NAG-NAG-MAN.11: 3 residues within 4Å: Chain B: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.12: 5 residues within 4Å: Chain B: N.1137, G.1138, T.1139, H.1140, F.1142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1140 NAG-NAG-MAN.13: 1 residues within 4Å: Chain B: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.19: 3 residues within 4Å: Chain C: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP)

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

NAG.26: 5 residues within 4Å: Chain A: P.369, N.370, I.371, P.618, Q.619 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain A: F.377, G.378, F.381, N.382, V.406, L.407 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: E.348, N.642 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: H.694, V.695, N.696 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.204, C.205 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: Y.67, N.100 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: N.655, T.657, Q.683 Chain B: A.885, R.886 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: P.369, N.370, I.371, P.618, Q.619 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: E.348, N.642 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain B: Y.67, N.69, F.98, S.99, N.100 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: N.655, T.657, Q.683 Chain C: A.885, R.886 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: H.694, V.695, N.696 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: P.369, N.370, I.371, P.618, Q.619 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: E.348, N.642 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: G.146, T.147, N.273, I.274, T.275 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: H.694, V.695, N.696 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: Y.67, T.68, N.69, N.100 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S. et al., Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct. J Struct Biol X (2025)

Release Date

2025-03-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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