SMTL ID : 7bno.1

Open conformation of D614G SARS-CoV-2 spike with 2 Erect RBDs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 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.748, L.953 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: Y.59, T.60, N.92 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: E.163, N.195, N.196 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: T.139, N.265, T.267 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.311, E.312, N.313 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.362, I.363, Q.611 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.634 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.647, C.648 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.740 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.832, S.834 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.1105 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: V.1164, N.1165 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: Y.59, N.92 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: E.163, N.195, N.196 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.311, E.312, N.313 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.634 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.647 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.740 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: T.747, N.748, Q.1102 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.832, S.834 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.1105 Chain C: Q.926 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1165 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: C.46, N.48, N.168 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: Y.59, N.61, N.92 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: S.143, E.163, N.195, N.196 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: E.312, N.313 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.634 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.647 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.740 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.748, N.950, Q.1102 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.832, S.834 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.1165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benton, D.J. et al., The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-02-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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