SMTL ID : 9og5.1

SARS-COV-2-6P-MUT7 S PROTEIN-DY-III-281 complex 1 RBD up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

homo-trimer

Ligands

14 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 C: F.342, N.343, S.371, S.373 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.371, C:S.373 NAG-NAG.2: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.3: 3 residues within 4Å: Chain B: N.343, V.367, W.436 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.367 NAG-NAG.4: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.5: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 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: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: N.1098, T.1100, F.1103, Y.1110, P.1112 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: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: K.795, N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain A: A.706, S.711, N.1074 Chain B: Q.895 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

1 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.12: 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

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

NAG.16: 3 residues within 4Å: Chain A: C.15, N.17, N.137 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.616, C.617 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: S.711, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: T.108, T.109, N.234, T.236 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: Q.895 Chain C: A.706, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandravanshi, M. et al., Optimization of VE607 to generate analogs with improved neutralization activities against SARS-CoV-2 variants. J.Virol. (2025)

Release Date

2025-10-01

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Spike glycoprotein

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