SMTL ID : 8epq.1

Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs exposed

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

11 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: 2 residues within 4Å: Chain A: N.691, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.317 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: H.1057, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: T.82, N.208 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: K.532 Chain B: E.255, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.691, L.896, Q.1045 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.896 NAG-NAG.10: 4 residues within 4Å: Chain B: N.96, T.98, V.101, F.131 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.691, L.896, Q.900, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.590, T.592 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: E.255, N.256 No protein-ligand interaction detected (PLIP)

4 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.2: 3 residues within 4Å: Chain A: N.254, E.255, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: N.775, S.777, N.902 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 5 residues within 4Å: Chain B: N.775, S.777, Q.778, N.902, G.906 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain C: N.775, Q.778, K.788, R.789 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.789, C:K.788, C:K.788

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

NAG.16: 4 residues within 4Å: Chain A: N.96, T.98, N.99, F.131 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.590, Q.618 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1048 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.20: 7 residues within 4Å: Chain A: T.82, T.88, N.208, T.210 Chain C: K.436, E.439, R.440 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.305 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.683, N.684 Chain B: D.770 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: Y.2, N.35 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: E.106, N.138, N.139 Chain C: R.440, I.442 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.26: 8 residues within 4Å: Chain A: V.1070, S.1071, N.1072, G.1073, T.1074, H.1075, W.1076, F.1077 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.1108 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.683 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.317 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.138, N.139 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: N.1072, T.1074, H.1075, F.1077, Y.1084 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: Y.2, N.35 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.590, Q.618, T.619 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.305 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: T.281, E.283, N.577 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.1048 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: A.866 Chain C: N.1048 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.305, I.306 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: H.629, V.630, N.631 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.35 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.138, N.139 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.1072, T.1074, H.1075, F.1077 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.208 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.577, T.578 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: G.313, F.316, N.317 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain A: D.770 Chain C: Y.681, N.683, N.684 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, J.A. et al., Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity. Sci Adv (2023)

Release Date

2023-06-21

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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