SMTL ID : 7xix.1

SARS-CoV-2 Omicron BA.2 variant spike (state 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

18 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.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.4: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.10: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.16: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.19: 7 residues within 4Å: Chain A: T.105, N.231, T.233 Chain C: N.457, L.458, K.459, E.462 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.340, N.367, F.368 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.58, W.255 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.119, A.120, T.121, N.122 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: S.109, N.162 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: S.708, N.1071 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain A: N.457, L.458, K.459, E.462 Chain B: T.105, N.231 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.340, N.367 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.58, W.255 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.119, A.120, T.121, N.122 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: S.109, E.129, N.162 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: S.708, N.1071 Ligand excluded by PLIP NAG.39: 7 residues within 4Å: Chain B: N.457, L.458, K.459, E.462 Chain C: T.105, N.231, T.233 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.340, N.367, F.368 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.58, W.255 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.119, A.120, T.121, N.122 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: S.109, E.129, N.162 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: S.708, N.1071 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Y. et al., BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature (2022)

Release Date

2022-07-13

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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