SMTL ID : 6z97.1

Structure of the prefusion SARS-CoV-2 spike glycoprotein

Coordinates

PDB Format

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: 7 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: K.458, S.459, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.717, F.718, L.922, N.925, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 4 residues within 4Å: Chain A: K.795, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1101 NAG-NAG.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.1098, G.1099, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1101 NAG-NAG.8: 4 residues within 4Å: Chain B: C.1082, I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain C: T.716, N.717, T.719, L.922, N.925, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.10: 4 residues within 4Å: Chain C: N.801, S.803, Q.804, Q.935 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.804 NAG-NAG.11: 6 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103, I.1114 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1101

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

NAG.12: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.343, V.367 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.709, N.710, I.1130, G.1131 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, V.367, L.368 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.709, I.1130, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: N.717, T.719, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain B: A.706, A.713, E.1072, K.1073, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.30, F.59, S.60, N.61 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.709, N.710, I.1130, G.1131 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain A: Q.895 Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, J. et al., Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike. Cell Host Microbe (2020)

Release Date

2020-07-01

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin

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