SMTL ID : 7bnm.1

Closed conformation of D614G SARS-CoV-2 spike protein

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: 4 residues within 4Å: Chain A: C.46, V.47, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.748, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1129, T.1131, H.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: Y.59, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: C.46, V.47, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.748, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.1129, T.1131, H.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: Y.59, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: C.46, V.47, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.748, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.1129, T.1131, H.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain C: N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: Y.59, N.92 No protein-ligand interaction detected (PLIP)

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

NAG.16: 3 residues within 4Å: Chain A: N.311, E.312, N.313 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain A: N.153, A.154, T.155, N.156, V.158, V.202 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.195, N.196 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: T.139, N.265, T.267 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.362, P.610, Q.611 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: F.369, G.370, F.373, N.374, S.402 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.647, T.649 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.688 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.740 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.832, S.834, Q.835 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: E.1103, K.1104, N.1105 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.311, E.312, N.313 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain B: N.153, A.154, T.155, N.156, V.158, V.202 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.195, N.196 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: T.139, N.265, T.267 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.362, P.610, Q.611 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain B: F.369, G.370, F.373, N.374, S.402 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.647, T.649 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.688 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.740 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.832, S.834, Q.835 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: E.1103, K.1104, N.1105 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.311, E.312, N.313 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain C: N.153, A.154, T.155, N.156, V.158, V.202 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.195, N.196 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: T.139, N.265, T.267 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.362, P.610, Q.611 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain C: F.369, G.370, F.373, N.374, S.402 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.647, T.649 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.688 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.740 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.832, S.834, Q.835 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: E.1103, K.1104, N.1105 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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