SMTL ID : 8epn.1

Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD Down conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

18 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: 1 residues within 4Å: Chain A: N.590 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.631 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.96, T.98, V.101 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.1072, T.1074, H.1075, F.1077, Y.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: A.680, S.682, S.685, N.1048 Chain B: L.868 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: N.305, Q.554 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.590 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain B: N.631 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: N.96, T.98, V.101 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain B: N.1072, T.1074, H.1075, F.1077, Y.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain B: A.680, S.682, S.685, N.1048 Chain C: L.868 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain B: N.305, Q.554 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 1 residues within 4Å: Chain C: N.590 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 1 residues within 4Å: Chain C: N.631 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.96, T.98, V.101 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain C: N.1072, T.1074, H.1075, F.1077, Y.1084 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain A: L.868 Chain C: A.680, S.685, N.1048 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 1 residues within 4Å: Chain C: N.305 No protein-ligand interaction detected (PLIP)

15 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.2: 2 residues within 4Å: Chain A: N.691, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 3 residues within 4Å: Chain A: N.254, N.256 Chain C: K.532 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 7 residues within 4Å: Chain A: F.316, N.317, A.346 Chain C: L.429, F.430, Y.463, Q.467 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.463 NAG-NAG-BMA-MAN-MAN.5: 4 residues within 4Å: Chain A: N.775, S.777, Q.778, N.902 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 1 residues within 4Å: Chain A: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 2 residues within 4Å: Chain B: N.691, Q.1045 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 3 residues within 4Å: Chain A: K.532 Chain B: N.254, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 7 residues within 4Å: Chain A: L.429, F.430, Y.463, Q.467 Chain B: F.316, N.317, A.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.463 NAG-NAG-BMA-MAN-MAN.16: 3 residues within 4Å: Chain B: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.20: 1 residues within 4Å: Chain B: N.1108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.24: 3 residues within 4Å: Chain C: N.691, L.896, Q.1045 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.896 NAG-NAG-BMA-MAN-MAN.25: 3 residues within 4Å: Chain B: K.532 Chain C: N.254, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.26: 7 residues within 4Å: Chain B: L.429, F.430, Y.463, Q.467 Chain C: F.316, N.317, A.346 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.463 NAG-NAG-BMA-MAN-MAN.27: 3 residues within 4Å: Chain C: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.31: 1 residues within 4Å: Chain C: N.1108 No protein-ligand interaction detected (PLIP)

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

NAG.34: 2 residues within 4Å: Chain A: N.683, N.684 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: V.282, E.283, T.576, N.577 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: E.106, N.138, N.139 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: Y.2, N.35 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: T.82, N.208, T.210 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.683 Chain C: I.768 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: V.282, E.283, T.576, N.577 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: N.138, N.139 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: Y.2, N.35 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: T.82, N.208, T.210 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.683 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: V.282, E.283, T.576, N.577 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.138, N.139 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: Y.2, N.35 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: T.82, N.208, T.210 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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