SMTL ID : 7tpi.1

SARS-CoV-2 E406W mutant Spike ectodomain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 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: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.3: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.5: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922

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

NAG.7: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: I.1132, N.1134 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: S.112, E.132, N.165 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.122, A.123, N.125 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: I.1132, N.1134 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: K.558 Chain B: N.282 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: S.112, E.132, N.165 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.122, A.123, N.125 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: I.1132, N.1134 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: K.558 Chain C: N.282 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: S.112, E.132, N.165 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.122, A.123, N.125 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Addetia, A. et al., SARS-CoV-2 E406W mutant Spike ectodomain. To Be Published

Release Date

2023-11-15

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein