SMTL ID : 7eb5.1

Cryo-EM structure of SARS-CoV-2 Spike D614G variant, two RBD-up conformation 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

27 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: T.108, N.234, I.235, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.616, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.709 Chain B: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: S.704, A.706, N.1074 Chain B: Q.895 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.8: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: K.558 Chain B: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.331, I.332, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.706 NAG-NAG.17: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: G.232, I.233, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain A: Q.895 Chain C: S.704, A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.28: 3 residues within 4Å: Chain A: T.29, N.30, N.61 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.122, T.124, N.125 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.122, T.124, N.125 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: T.114, Q.115, E.132, N.165 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: I.233, N.234 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.122, T.124 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Q.115, N.165 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. J.Biol.Chem. (2021)

Release Date

2021-06-23

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Spike glycoprotein

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