SMTL ID : 7kdl.1

SARS-CoV-2 D614G 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.280, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain B: V.120, N.122, A.123, T.124, V.127, K.129 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: T.108, N.234 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: I.794 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: E.1072, N.1074 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: G.339, N.343, L.368 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: F.59, N.61 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: E.1072, N.1074 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.126, V.127, V.171 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Cell Rep (2021)

Release Date

2020-11-04

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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