SMTL ID : 7t67.1

SARS-CoV-2 S (Spike Glycoprotein) D614G with One(1) RBD Up

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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: N.717, T.719, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.717, T.719, L.922, Q.926 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.3: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, V.171 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.10: 9 residues within 4Å: Chain A: G.339, F.342, N.343, V.367, L.368, S.371, A.372, S.373, F.374 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain B: N.122, T.124, N.125, V.126, V.127, V.171 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: D.796 Chain B: N.709 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: F.338, G.339, N.343 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.126, V.127, V.171 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: G.232, N.234 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: D.796 Chain C: N.709 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.343 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Byrne, P.O. et al., SARS-CoV-2 S (Spike Glycoprotein) D614G with One(1) RBD Up. To Be Published

Release Date

2022-08-24

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
G

Spike glycoprotein

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