SMTL ID : 7xiw.1

SARS-CoV-2 Omicron BA.2 variant spike (state 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.62 Å

Oligo State

homo-trimer

Ligands

13 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: D.336, N.340, N.367, F.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.367 NAG-NAG.2: 2 residues within 4Å: Chain A: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: D.336, N.340, N.367, F.368 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.714, L.919 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.8: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.714, L.919 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.12: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 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)(Non-covalent)(Non-functional Binders)

NAG.14: 2 residues within 4Å: Chain A: N.58, W.255 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.119, V.124 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.161, N.162 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.613, T.615 Chain B: I.831 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.1071 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: Y.25, N.58, T.60, W.255 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.119, A.120, T.121, N.122 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: E.129, N.161, N.162 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: R.454 Chain B: T.105, N.231 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.613, T.615 Chain C: I.831 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.706 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1071 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: Y.25, N.58, T.60, W.255 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.119, N.122, V.124 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: E.129, N.161, N.162 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: R.454 Chain C: T.105, N.231 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: I.831, Q.833 Chain C: N.613 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.798, S.800 Ligands: NAG.42 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Ligands: NAG.41 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: 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
D

Spike glycoprotein

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