SMTL ID : 8epp.1

Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs in the open conformation

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: 3 residues within 4Å: Chain A: C.1056, C.1100, N.1108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1108 NAG-NAG.5: 4 residues within 4Å: Chain B: N.691, L.896, Q.900, Q.1045 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.896 NAG-NAG.7: 2 residues within 4Å: Chain B: N.590, Q.618 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: S.678, A.680, Y.1046, N.1048 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: C.1056, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.691, L.896, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.590, T.592, E.593 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: C.1056, H.1057, N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain C: N.96, A.97, T.98, N.99, V.101, K.103 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.98

3 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.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 1 residues within 4Å: Chain A: N.691 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 1 residues within 4Å: Chain B: N.256 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.4: 3 residues within 4Å: Chain A: E.255, N.256 Chain C: K.532 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 3 residues within 4Å: Chain B: N.775, S.777, Q.778 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.778, B:Q.778 NAG-NAG-BMA-MAN-MAN.12: 3 residues within 4Å: Chain C: N.775, S.777, Q.778 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.778

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

NAG.16: 2 residues within 4Å: Chain A: F.33, N.35 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: N.96, T.98, N.99, V.101, E.128 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.683 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: F.1049, N.1072, H.1075, F.1077, Y.1084 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: E.106, N.139 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.317, S.345 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: Y.1046, N.1048 Chain B: A.866, L.868 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: K.436, E.439 Chain B: T.82, N.208 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain B: N.96, T.98, N.99, V.101, F.131 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.631, N.632 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.317 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.683, G.1105 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: S.34, N.35 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain A: L.868 Chain C: A.680, S.682, S.685, N.1048 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.1072, T.1074, H.1075, F.1077 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: D.770 Chain C: N.683 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.631 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: T.281, N.577 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: G.313, N.317, S.345, S.347 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.255, N.256 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.138, N.139 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: G.173, N.208 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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