SMTL ID : 7eaz.1

Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain B: G.232, I.233, N.234 No protein-ligand interaction detected (PLIP)

30 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.2: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.331, I.332, Q.580, T.581 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.581 NAG-NAG.4: 2 residues within 4Å: Chain A: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.9: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain B: N.616 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: S.708, N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain B: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: N.234, I.235, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: S.708, N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain C: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.706 NAG-NAG.31: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

16 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.33: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.122, N.125 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.343, W.436 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: N.122, T.124, N.125 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.122, T.124, N.125 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.48: 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
A

B
B

C
C

Spike glycoprotein

Related Entries With Identical Sequence