SMTL ID : 7yqu.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.19 Å

Oligo State

homo-trimer

Ligands

6 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: 2 residues within 4Å: Chain A: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: Y.25, F.56, N.58 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.119, T.121, N.122, V.124 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.161, N.162 Chain B: I.465 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: N.231 Chain B: R.454, S.456, K.459, E.462 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.340, A.341, L.438 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain A: N.613, E.616 Chain C: K.832, Q.833, Y.834, D.836 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: Y.25, F.56, N.58 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.119, T.121, N.122, V.124 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.161, N.162 Chain C: I.465 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain B: N.231 Chain C: R.454, S.456, K.459, E.462 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.340, A.341, L.438 Ligand excluded by PLIP NAG.26: 6 residues within 4Å: Chain A: K.832, Q.833, Y.834, D.836 Chain B: N.613, E.616 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: Y.793 Chain B: N.706 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: Y.25, F.56, N.58 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.119, T.121, N.122, V.124 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: I.465 Chain C: N.161, N.162 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain A: R.454, S.456, K.457, K.459, E.462 Chain C: N.231 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.340, A.341, L.438 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain B: K.832, Q.833, Y.834, D.836 Chain C: N.613, E.616 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.42: 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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Spike glycoprotein