SMTL ID : 9cxe.1

SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation -C1

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 A: Q.934 Chain C: S.743, A.745, 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.8: 8 residues within 4Å: Chain A: S.743, A.745, S.747, S.750, E.1111, K.1112, N.1113 Chain B: Q.934 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 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)

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

NAG-NAG.2: 4 residues within 4Å: Chain A: N.748, I.1169, G.1170 Chain B: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.840, S.842, Q.843, Q.974 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 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.12: 1 residues within 4Å: Chain B: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.748, I.1169, G.1170 Chain C: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: N.840, S.842, Q.843, Q.974 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain A: D.835 Chain C: N.748, I.1169, G.1170 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain A: A.885, R.886 Chain C: N.655, T.657, E.658 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: G.378, F.381, N.382 No protein-ligand interaction detected (PLIP)

11 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.3: 3 residues within 4Å: Chain A: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 5 residues within 4Å: Chain A: N.319, E.320, N.321, T.323, T.325 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 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.7: 4 residues within 4Å: Chain A: C.1165, D.1166, I.1171, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 2 residues within 4Å: Chain B: N.319, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 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.16: 8 residues within 4Å: Chain A: F.495, N.526, Y.528 Chain B: F.381, N.382, V.406, S.410, F.413 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.410 NAG-NAG-BMA.17: 4 residues within 4Å: Chain C: N.319, E.320, N.321, T.325 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 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.20: 1 residues within 4Å: Chain C: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 7 residues within 4Å: Chain C: N.756, F.757, T.758, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.961

1 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.5: 6 residues within 4Å: Chain A: T.755, N.756, L.961, N.964, Q.965, Q.1110 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.961

15 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.25: 5 residues within 4Å: Chain A: P.369, N.370, I.371, P.618, Q.619 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.348, N.642 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: H.694, V.695, N.696 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: N.655, T.657, Q.683 Chain B: A.885, R.886 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: G.378, F.381, N.382 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: P.369, N.370, I.371, P.618, Q.619 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.642 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain B: Y.67, T.68, N.69, F.98, N.100 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: N.655, T.657, Q.683 Chain C: A.885, R.886 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: H.694, V.695, N.696 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: P.369, N.370, I.371, Q.619 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.642 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain C: G.146, T.147, N.273, I.274, T.275 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: H.694, V.695, N.696 Ligand excluded by PLIP NAG.39: 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