SMTL ID : 9atq.1

XBB.1.5 spike/Nanosota-8 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

16 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.700, L.905, Q.909, Q.1054 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.905 NAG-NAG.2: 3 residues within 4Å: Chain A: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: A.689, E.1055, K.1056, N.1057 Chain B: Q.878 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.700, L.905, Q.909, Q.1054 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: A.689, E.1055, K.1056, N.1057 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.689 NAG-NAG.9: 4 residues within 4Å: Chain B: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1117 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain C: N.106, A.107, T.108, N.109, V.111, E.137 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.700, L.905, Q.909, Q.1054 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.905 NAG-NAG.13: 3 residues within 4Å: Chain C: N.784, S.786, Q.787 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: A.689, E.1055, N.1057 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1117 No protein-ligand interaction detected (PLIP)

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

NAG.17: 2 residues within 4Å: Chain A: Y.12, N.45 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.148 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: T.92, N.217, T.219 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.264, N.265 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: H.322, N.326 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.692 Chain B: I.777, Y.779 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Y.12, N.45 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.148 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: T.92, N.217, T.219 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: K.541 Chain B: N.263, E.264, N.265 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.314, I.315 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: S.691, N.692 Chain C: Y.779 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: Y.12, N.45 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: E.116, N.148 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: E.448 Chain C: T.92, N.217 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.263, E.264, N.265 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.314, P.562, Q.563 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.326 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: Y.779 Chain C: N.692 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Structure of XBB.1.5 spike and Nanosota-8 complex. To Be Published

Release Date

2025-08-27

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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