SMTL ID : 8v0p.1

SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-XBB.1.16)

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.713, L.918, Q.922, Q.1067 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.918 NAG-NAG.2: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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.5: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.713, L.918 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.1094, H.1097, F.1099 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: Y.25, N.27, N.58 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.276, E.277, N.278 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.327, Q.576 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: H.335, N.339 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.612, T.614, Q.640 Chain B: Q.832 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.705 Chain B: I.790, Y.792 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: Y.25, N.27, N.58 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: C.128, E.129, N.161 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.276, E.277, N.278 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.327, Q.576 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: H.335, N.339 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.612, Q.640 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.705 Chain C: I.790, Y.792 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: A.702, N.1070 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.1130 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: R.453, K.458 Chain B: T.105, N.230, T.232 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: K.458 Chain C: T.105, N.230, T.232 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.230 Chain C: S.455, K.458 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: E.277, N.278 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.327 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.339, F.367 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.612, T.614 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: Y.792 Chain C: N.705, I.1126 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: A.702, N.1070 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: Q.112, C.128, E.129, N.161 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Q.E. et al., SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition. Mol.Cell (2024)

Release Date

2024-06-12

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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