SMTL ID : 9b2v.1

SARS CoV-2 Spike protein Ectodomain with internal tag, 1RBD-up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 4 residues within 4Å: Chain A: N.319, E.320, N.321 Chain C: K.597 No protein-ligand interaction detected (PLIP)

10 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: 3 residues within 4Å: Chain A: G.378, N.382, S.412 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.655, T.657, Q.683 Chain B: A.885, R.886, D.887 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.748, I.1169, G.1170 Chain B: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain A: A.745, S.750, A.752, N.1113, F.1114, T.1115 Chain B: Q.934 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.934, B:Q.934, A:N.1113 NAG-NAG.11: 4 residues within 4Å: Chain B: G.378, N.382, S.410, S.412 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.410 NAG-NAG.12: 4 residues within 4Å: Chain B: N.748, I.1169, G.1170 Chain C: D.835 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: S.85, E.320, N.321 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.23: 2 residues within 4Å: Chain C: T.147, N.273 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain C: G.378, F.381, N.382, S.410 No protein-ligand interaction detected (PLIP)

14 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: 8 residues within 4Å: Chain A: T.755, 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-BMA.6: 3 residues within 4Å: Chain A: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain A: N.370, P.618, Q.619, L.621 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 1 residues within 4Å: Chain A: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain B: V.1172, N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain B: N.840, S.842, Q.843 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain B: N.756, F.757, L.961, N.964, Q.965, Q.1110 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.961, B:N.964, B:Q.965 NAG-NAG-BMA.16: 5 residues within 4Å: Chain B: N.1137, G.1138, T.1139, H.1140, F.1142 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 6 residues within 4Å: Chain C: N.756, F.757, T.758, L.961, Q.965, Q.1110 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.22: 5 residues within 4Å: Chain A: A.885, R.886 Chain C: N.655, T.657, Q.683 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 4 residues within 4Å: Chain B: K.597 Chain C: N.319, E.320, N.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 1 residues within 4Å: Chain C: N.1173 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 4 residues within 4Å: Chain C: N.840, S.842, Q.843, N.967 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.5: 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

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.19: 4 residues within 4Å: Chain A: Q.934 Chain C: A.745, K.1112, N.1113 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1113

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

NAG.28: 5 residues within 4Å: Chain A: Y.67, N.69, F.98, S.99, N.100 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: T.147, T.148, N.273, T.275 Chain C: E.504 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.642, T.643 Ligand excluded by PLIP NAG.31: 12 residues within 4Å: Chain A: N.138, R.141, N.160, N.161, A.162, T.163, N.164, V.165, P.213, F.214, L.215, M.216 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain A: N.161, A.162, T.163, V.166, K.168, M.192 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: H.694, V.695, N.696 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.204, C.205 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: T.147, N.273 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.642, T.643 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.696 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain B: Q.154, C.170, E.171, N.204, C.205, T.206 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: P.369, N.370, P.618, Q.619, T.620, L.621 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: Y.67, N.100 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain B: N.655, T.657, Q.683 Chain C: I.873, Q.875 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.370, Q.619, T.620 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: S.99, N.100 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.642, T.643 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: H.694, V.695, N.696 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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