SMTL ID : 7yqz.1

SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state3)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.84 Å

Oligo State

hetero-3-2-2-mer

Ligands

2 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 8 residues within 4Å: Chain A: F.335, F.339, N.340, F.368 Chain F: Y.100, D.115 Chain G: Y.50, R.55 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.115, F:D.115 NAG-NAG-BMA-FUC.2: 8 residues within 4Å: Chain B: F.339, N.340, F.368 Chain D: Y.100, D.115 Chain E: L.47, Y.50, R.55 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:D.115 Hydrophobic interactions: E:L.47, E:Y.50

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

NAG.3: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.119, T.121, N.122 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.161, N.162 Chain B: I.465 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: T.105, N.231, T.233 Chain B: R.454, E.462 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.279 Chain B: K.555 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.600, T.601 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.613, T.615, E.616 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.714, Q.1068 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: A.703, N.1071 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: Y.25, T.26, N.27, N.58 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.119, T.121, V.124 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: T.105, N.231, T.233 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.279 Chain C: K.555 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: Q.892 Chain B: E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.161, N.162 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.613, T.615, E.616 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.706 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.714 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.798, S.800 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.119, V.124 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.161, N.162 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: T.105, N.231 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.277, N.279 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.613, T.615, E.616 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.714 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: K.1070, N.1071 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.1095, H.1098, F.1100 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.1131 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
S309 heavy chain: DF
S309 light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
I

F
J

E
G

G
H

Spike glycoprotein

S309 heavy chain

S309 light chain

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