SMTL ID : 9og4.1

SARS-COV-2-6P-MUT7 S PROTEIN-DY-III-281 complex closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.56 Å

Oligo State

homo-trimer

Ligands

13 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: 1 residues within 4Å: Chain C: N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.709, N.710, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: Q.895 Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 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.9: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 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: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.709 Chain C: I.794, D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain A: N.709, N.710 Chain B: D.796 No protein-ligand interaction detected (PLIP)

7 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.3: 3 residues within 4Å: Chain C: K.795, N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 6 residues within 4Å: Chain A: N.487, Y.489 Chain B: G.339, F.342, N.343, L.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.489 NAG-NAG-BMA.15: 4 residues within 4Å: Chain A: T.108, T.109, N.234, T.236 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.109 NAG-NAG-BMA.16: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 5 residues within 4Å: Chain A: N.717, F.718, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1101

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

NAG.21: 5 residues within 4Å: Chain A: Q.14, C.15, N.17, C.136, N.137 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.331, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: A.706, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.616 Chain C: R.847 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: A.706, S.711, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.126, V.127 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: A.163, N.164, N.165 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: T.108, T.109, T.114, N.234 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: N.122, A.123, N.125, V.127 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: R.457, E.465 Chain C: N.234, T.236 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: A.845 Chain C: N.616, C.617, T.618 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.657 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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