SMTL ID : 9f9y.1

SARS-CoV-2 BA-2.87.1 Spike ectodomain

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: 4 residues within 4Å: Chain A: N.692, L.897, Q.901, Q.1046 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.897 NAG-NAG.2: 3 residues within 4Å: Chain A: N.776, S.778, Q.779 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1073, T.1075, H.1076, F.1078 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.692, L.897, Q.901, Q.1046 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.897 NAG-NAG.5: 3 residues within 4Å: Chain B: N.776, S.778, Q.779 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1073, T.1075, H.1076, F.1078 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.692, L.897, Q.901, Q.1046 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.897 NAG-NAG.8: 3 residues within 4Å: Chain C: N.776, S.778, Q.779 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1073, T.1075, H.1076, F.1078 No protein-ligand interaction detected (PLIP)

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

NAG.10: 2 residues within 4Å: Chain A: F.47, N.49 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.108, T.110, V.113 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.139, N.140 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.163, H.182, P.184 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: T.94, N.209 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.255, E.256, N.257 Chain B: K.533 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.306, P.554, Q.555 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.318, F.346 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.591, Q.619 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: Y.630, N.632 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.684, G.1106 Chain C: H.771 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.1049, F.1050, T.1051 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.1109 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: F.47, N.49, P.606 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.108, T.110, V.113 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.139, N.140 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.163, H.182, P.184 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: T.94, N.209 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.255, E.256, N.257 Chain C: K.533 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.306, P.554, Q.555 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.318, F.346 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.591, Q.619 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: Y.630, N.632 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: H.771 Chain B: N.684, G.1106 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.1049, F.1050, T.1051 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.1109 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: F.47, N.49, P.606 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.108, T.110, V.113 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.139, N.140 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.163, H.182, P.184 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: T.94, N.209 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: K.533 Chain C: N.255, E.256, N.257 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.306, P.554, Q.555 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.318, F.346 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.591, Q.619 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: Y.630, N.632 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: H.771 Chain C: N.684, G.1106 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.1049, F.1050, T.1051 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.1109 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duyvesteyn, H.M.E. et al., Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike. Structure (2024)

Release Date

2024-08-21

Peptides

Spike glycoprotein,Fibritin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,Fibritin