SMTL ID : 7yqv.1

pH 5.5 SARS-CoV-2 BA.2.75 S Trimer (1 RBD Up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 2 residues within 4Å: Chain A: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.714 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain C: N.798 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: A.703, N.1071 No protein-ligand interaction detected (PLIP)

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

NAG.10: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: T.70, N.71 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.119, L.154 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.146 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.162 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain A: T.105, N.231, I.232, T.233 Chain C: R.454, D.464 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.328, T.578 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.340, A.341, F.368 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.613, T.615, E.616 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: Y.25, N.58, W.255 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.71, V.140 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.119, A.120, T.121 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.146 Ligand excluded by PLIP NAG.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: T.105, N.231 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: 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: 4 residues within 4Å: Chain B: N.613, T.615 Chain C: I.831, Q.833 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: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: I.1129, N.1131 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: Y.25, F.56, N.58 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.71 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.119, A.120, N.122 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.146 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.161, N.162 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain B: D.464 Chain C: T.105, I.230, N.231, T.233 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: K.555 Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: H.336, F.339, N.340, A.341 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain A: I.831 Chain C: N.613, T.615 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.706 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.54: 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
A

B
B

C
C

Spike glycoprotein

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