SMTL ID : 9og7.1

APO SARS-COV-2-6P-MUT7 S PROTEIN 1 RBD UP CONFORMATION

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.09 Å

Oligo State

homo-trimer

Ligands

16 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.709, N.710, I.1130, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 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.4: 2 residues within 4Å: Chain A: K.558 Chain B: N.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.558 NAG-NAG.6: 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.7: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: S.704, A.706, E.1072, N.1074 Chain B: Q.895 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.706 Hydrogen bonds: A:S.704 NAG-NAG.9: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: C.1082, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: T.108, T.114, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 9 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.458, B:K.458 NAG-NAG.21: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP)

5 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.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain B: F.456, N.487, Y.489 Chain C: N.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.487, B:Y.489, B:Y.489 NAG-NAG-BMA.17: 6 residues within 4Å: Chain B: N.717, F.718, T.719, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain B: K.795, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.15: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.23: 4 residues within 4Å: Chain A: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.122, T.124, N.125, Q.173 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: E.132, N.164, N.165 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: T.108, N.234 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.616, C.617, Q.644 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: A.706, E.1072, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: P.330, N.331, P.579, Q.580 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.616, T.618, E.619 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: Q.895 Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: Y.351 Chain C: N.164, N.165 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.30, F.59, N.61, P.631 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.122, S.155 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: N.17, C.136, N.137, D.138, R.158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, L. 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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