SMTL ID : 9d8i.1

JN.1 SARS-COV-2 Spike 1-up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

17 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.277, E.278, N.279 Chain C: K.554 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.328, P.575, Q.576, L.578 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.705 Chain B: I.790, Y.792 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.713, L.918, Q.1067 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.918 NAG-NAG.5: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: K.554 Chain B: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.705 Chain C: I.790, Y.792 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.792 NAG-NAG.10: 4 residues within 4Å: Chain B: N.713, L.918, Q.922, Q.1067 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.918 NAG-NAG.11: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.612, Q.640 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain B: E.337, R.343, F.344, A.345, N.351, T.353 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.337 NAG-NAG.16: 4 residues within 4Å: Chain A: I.790, Y.792 Chain C: N.705, I.1126 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.713, L.918, Q.922, Q.1067 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.922 NAG-NAG.18: 4 residues within 4Å: Chain A: Q.891 Chain C: E.1068, K.1069, N.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain C: E.337, A.341, N.351, R.352, R.463 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain B: K.554 Chain C: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-FUC.6: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.7: 1 residues within 4Å: Chain A: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.12: 5 residues within 4Å: Chain B: N.1094, T.1096, H.1097, F.1099, P.1108 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.1099, B:P.1108 NAG-NAG-FUC.13: 1 residues within 4Å: Chain B: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.19: 3 residues within 4Å: Chain C: N.1094, H.1097, F.1099 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.1099 NAG-NAG-FUC.20: 1 residues within 4Å: Chain C: N.1130 No protein-ligand interaction detected (PLIP)

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

NAG.24: 3 residues within 4Å: Chain A: N.340, A.341, T.342 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.599, T.600 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: A.702, E.1068, K.1069, N.1070 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.612, Q.640 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: T.107, N.231, T.233 Chain C: E.462 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: Y.29, F.60, N.62 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: N.121, T.123, F.126, E.152, E.154 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: S.111, E.131, N.162, N.163 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.351, R.352, T.353 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.599 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: A.702, E.1068, N.1070 Chain C: Q.891 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: G.229, N.231 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: N.121, T.123, F.126, E.154 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: Y.29, N.62 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.328, Q.576, L.578 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.340, F.368 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.328, P.575, Q.576 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: Q.832 Chain C: N.612, T.614, Q.640 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: E.462 Chain C: T.107, N.231, T.233 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.121, T.123, F.126, E.154 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: E.131, N.162, N.163 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.340 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.599, T.600 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: Y.29, N.62 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Windsor, I.W. et al., SARS-CoV-2 JN.1 and KP.2 spike characteristics and neutralization of JN.1-derived sublineages and T cell responses from mice immunized with monovalent JN.1- and KP.2-adapted BNT162b2 COVID-19 vaccines. To Be Published

Release Date

2025-10-29

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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