SMTL ID : 8x5q.1

SARS-CoV-2 BA.2.75 Spike with K356T mutation (3 RBD down)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

21 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.119, N.122, V.124 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.161, N.162 Chain C: Y.348, I.465 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.231 Chain C: K.455, S.456, K.459 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.456, C:S.456 NAG-NAG.4: 2 residues within 4Å: Chain A: H.336, N.340 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: E.337, V.338, N.351, T.353 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.119, N.122, V.124 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: Y.348, I.465 Chain B: N.161, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: K.455, S.456, K.459 Chain B: N.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.455, A:K.455, A:S.456, A:S.456 NAG-NAG.11: 2 residues within 4Å: Chain B: H.336, N.340 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.351, R.352, T.353 Chain C: T.164 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.119, N.122, V.124 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: Y.348, I.465 Chain C: N.161, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: K.455, S.456, K.459 Chain C: N.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.456, B:S.456 NAG-NAG.18: 2 residues within 4Å: Chain C: H.336, N.340 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain A: T.164 Chain C: N.351, R.352, T.353 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.22: 3 residues within 4Å: Chain A: Y.25, N.58, W.255 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: Y.704, S.705, N.706 Chain B: I.791, Y.793 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.613 Chain B: I.831, Q.833 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: Y.25, N.58, W.255 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: S.705, N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.613 Chain C: I.831, Q.833 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: I.831, Q.833 Chain C: N.613 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: Y.25, N.58, W.255 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.279 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain A: I.791, Y.793 Chain C: Y.704, S.705, N.706 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, P. et al., Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity. Natl Sci Rev (2024)

Release Date

2024-07-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Spike glycoprotein

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