SMTL ID : 8ios.1

Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-1 state)

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.712, L.917 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1093, T.1095, H.1096, F.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.712, L.917 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1093, T.1095, H.1096, F.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.712, L.917 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1093, T.1095, H.1096, F.1098 No protein-ligand interaction detected (PLIP)

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

NAG.10: 4 residues within 4Å: Chain A: Y.24, T.25, N.26, N.57 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.159, N.160 Ligand excluded by PLIP NAG.13: 7 residues within 4Å: Chain A: T.104, N.229, T.231 Chain C: R.452, S.454, K.455, K.457 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.275, E.276, N.277 Chain C: K.553 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.326, Q.575 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: H.334, N.338, F.366 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.611, T.613 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.652 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: Y.702, S.703, N.704 Chain B: Y.791 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: E.1067, N.1069 Chain B: Q.890 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.1129 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: Y.24, T.25, N.26, N.57 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.159, N.160 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain A: R.452, S.454, K.455, K.457 Chain B: T.104, N.229, T.231 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: K.553 Chain B: N.275, E.276, N.277 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.326, Q.575 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: H.334, N.338, F.366 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.611, T.613 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.652 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: Y.702, S.703, N.704 Chain C: Y.791 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: E.1067, N.1069 Chain C: Q.890 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.1129 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: Y.24, T.25, N.26, N.57 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.159, N.160 Ligand excluded by PLIP NAG.37: 7 residues within 4Å: Chain B: R.452, S.454, K.455, K.457 Chain C: T.104, N.229, T.231 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: K.553 Chain C: N.275, E.276, N.277 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.326, Q.575 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: H.334, N.338, F.366 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.611, T.613 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.652 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain A: Y.791 Chain C: Y.702, S.703, N.704 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: Q.890 Chain C: E.1067, N.1069 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.1129 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamura, T. et al., Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun (2023)

Release Date

2023-05-24

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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