SMTL ID : 7tb4.1

Cryo-EM structure of the spike of SARS-CoV-2 Omicron variant of concern

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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: 3 residues within 4Å: Chain A: N.701, L.906, Q.910 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: S.688, A.690, N.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.1082, T.1084, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.701, L.906, Q.910, Q.1055 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.906 NAG-NAG.7: 3 residues within 4Å: Chain B: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.1082, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: Y.780 Chain C: N.693, I.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: T.700, N.701, L.906, Q.1055 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.906 NAG-NAG.12: 3 residues within 4Å: Chain C: N.1082, T.1084, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.315, I.316, Q.564, L.566 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.266 Chain C: K.542 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.315, Q.564 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: D.323, F.326, N.327 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.641 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.693 Chain B: I.778, Y.780 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: N.107, A.108, T.109, N.110, V.112 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.117, N.146, N.147 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.218 Chain C: H.503 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.600 Chain B: I.818, Q.820 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: E.293, K.294, G.585, N.587 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.264, E.265, N.266 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.693 Chain C: Y.780 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.315, Q.564 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: F.322, D.323, N.327, N.354 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.600, Q.628 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.641 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: E.293, N.587 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain A: R.441, S.443, N.444, K.446, E.449 Chain B: N.218 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: A.690, N.1058 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: Y.639, N.641 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.293, N.587 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain B: K.542 Chain C: N.264, E.265, N.266, T.268 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.218 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: V.105, N.107, T.109, N.110, V.112 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants. Biorxiv (2021)

Release Date

2022-01-12

Peptides

Surface glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Surface glycoprotein