SMTL ID : 7yqw.1

SARS-CoV-2 BA.2.75 S Trimer (3 RBD Down)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.51 Å

Oligo State

homo-trimer

Ligands

6 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.1: 2 residues within 4Å: Chain A: N.714, L.919 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain B: N.714, L.919 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG-BMA.9: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain C: N.714, L.919 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG-BMA.14: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

9 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.1071 Chain B: Q.892 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.1071 Chain C: Q.892 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain A: Q.892 Chain C: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.119, T.121, N.122, V.124 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.162 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: T.105, N.231 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: H.336, N.340 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: S.705, N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.119, T.121, N.122, V.124 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.162 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: T.105, N.231 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: H.336, N.340 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: S.705, N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.119, T.121, N.122, V.124 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.162 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: T.105, N.231 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: H.336, N.340 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.613, T.615 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain A: Y.793 Chain C: S.705, N.706 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Y. et al., Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75. Cell Host Microbe (2022)

Release Date

2022-10-19

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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