SMTL ID : 9og6.1

Apo SARS-COV-2-6P-MUT7 S PROTEIN closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.14 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: 10 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, L.461, K.462, E.465 Chain C: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.459 NAG-NAG.2: 3 residues within 4Å: Chain B: F.338, G.339, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.343, S.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.373, A:S.373 NAG-NAG.4: 3 residues within 4Å: Chain A: N.709, N.710, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 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.7: 3 residues within 4Å: Chain A: K.558 Chain B: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 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.10: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: A.706, E.1072, N.1074 Chain B: Q.895 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain A: C.1082, H.1083, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain A: I.794, D.796 Chain C: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain A: K.462, E.465, D.467 Chain B: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.709 Chain C: I.794, D.796 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.5: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain B: F.456, Y.489 Chain C: F.342, N.343, V.367 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.489 NAG-NAG-BMA.20: 5 residues within 4Å: Chain B: N.717, T.719, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 3 residues within 4Å: Chain B: N.1098, 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.18: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.23: 4 residues within 4Å: Chain A: Y.28, N.30, F.59, N.61 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.122, N.125, F.157, Q.173 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: N.280, N.282, T.284 Chain C: K.558 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.137 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: A.706, E.1072, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain A: G.842, A.846, R.847 Chain C: N.616, T.618, E.619 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: Q.895 Chain C: E.1072, N.1074 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: K.558 Chain C: E.281, N.282 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: Y.351, I.468 Chain C: N.164, N.165 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.30, F.59, N.61, P.631 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.17, C.136, 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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