SMTL ID : 7y6d.1

Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: F.338, G.339, N.343, S.371, A.372, S.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.372, A:S.373 NAG-NAG.6: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain B: F.338, G.339, N.343, S.371, A.372, S.373 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.372, B:S.373 NAG-NAG.11: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain C: F.338, G.339, N.343, S.371, A.372, S.373 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.372, C:S.373

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

NAG.16: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: E.465, R.466 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.616, Q.644 Chain B: I.834 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: E.465, R.466 Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.616, Q.644 Chain C: I.834 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: E.132, N.164, N.165 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain B: E.465, R.466 Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: I.834 Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, Y. et al., In situ architecture and membrane fusion of SARS-CoV-2 Delta variant. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-06-07

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein