SMTL ID : 8gs6.1

Structure of the SARS-CoV-2 BA.2.75 spike glycoprotein (closed state 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

5 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: 1 residues within 4Å: Chain A: N.797 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.713, Q.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.713, L.918 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.918 NAG-NAG.4: 3 residues within 4Å: Chain C: N.713, L.918, Q.922 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.918 NAG-NAG.5: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: Y.24, N.57 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.327 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.339, F.367 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.612 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.705 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: E.1068, N.1070 Chain B: Q.891 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.13: 7 residues within 4Å: Chain A: T.104, N.230 Chain C: R.453, K.454, K.456, K.458, E.461 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.160, N.161 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.276, E.277, N.278 Chain C: K.554 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.327 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: H.335, N.339, F.367 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.612, Q.640 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1130 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.705 Chain C: Y.792 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: K.554 Chain B: N.276, E.277, N.278 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.1094, T.1096, F.1099 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.797, S.799 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: Y.24, N.57 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: K.554 Chain C: E.277, N.278 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.327, Q.576 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: H.335, N.339 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: K.831 Chain C: N.612, T.614 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: I.790, Y.792 Chain C: N.705 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.1068, N.1070 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.192, N.230, I.231, T.232 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.1094, F.1099 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saito, A. et al., Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant. Cell Host Microbe (2022)

Release Date

2022-10-26

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein