SMTL ID : 7bnn.1

Open conformation of D614G SARS-CoV-2 spike with 1 Erect RBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

7 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.740 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.748, L.953 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1129, T.1131, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.748, T.750, Q.957, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1129, T.1131, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.748, L.953, Q.957 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.832, S.834, Q.835 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 3 residues within 4Å: Chain A: A.737, N.1105 Chain B: Q.926 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1105

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

NAG.9: 4 residues within 4Å: Chain A: C.46, V.47, N.48, N.168 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: Y.59, N.92 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: T.139, N.265, I.266, T.267 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: E.312, N.313 Chain C: K.589 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.362, P.610, Q.611 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: G.370, F.373, N.374, S.402, A.403 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.634 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.647, T.649 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.688 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.832, S.834, Q.835 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: I.1163, N.1165 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: C.46, V.47, N.48, N.168 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: Y.59, T.60, N.92 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.195, N.196 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: T.139, N.265, T.267 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: E.312, N.313 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.362, T.364, Q.611 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.634 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.647, T.649 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.688 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.740, N.741 Chain C: D.827 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.832, S.834 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: E.1103, K.1104, N.1105 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1165 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.1165 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.1129, G.1130, T.1131, H.1132 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: E.1103, K.1104, N.1105 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: T.139, N.265 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.313 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.634 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.647 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.688 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: D.827 Chain C: N.740, G.1162 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