SMTL ID : 7xnq.1

SARS-CoV-2 Omicron BA.4 variant spike

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: 4 residues within 4Å: Chain A: N.275, E.276, N.277 Chain C: K.553 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.704 Chain B: Y.791 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.712, Q.921, Q.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: S.699, S.706, N.1069 Chain B: Q.890 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.699 NAG-NAG.6: 1 residues within 4Å: Chain A: N.1129 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: K.553 Chain B: E.276, N.277 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.704 Chain C: Y.791 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.712, L.917, Q.921, Q.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: S.699, N.1069 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.699 NAG-NAG.12: 1 residues within 4Å: Chain B: N.1129 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: K.553 Chain C: E.276, N.277 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain A: Y.791 Chain C: N.704 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.712, Q.921, Q.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain A: Q.890 Chain C: S.699, N.1069 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.699 NAG-NAG.18: 1 residues within 4Å: Chain C: N.1129 No protein-ligand interaction detected (PLIP)

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

NAG.19: 4 residues within 4Å: Chain A: N.58, V.59, T.60, W.253 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: G.67, N.69, Y.139, S.242 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.117, T.119, N.120, V.122 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.144, W.147 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: E.127, N.160 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: N.229 Chain C: R.452, E.460, R.461, D.462 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.326, T.576 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.598 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.611, T.613, E.614 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.652 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.58, T.60, W.253 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: G.67, N.69 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.117, N.120, V.122 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.144, W.147 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: E.127, N.160 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain A: R.452, E.460, R.461, D.462 Chain B: N.229 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.326, T.576 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.598 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.611, T.613, E.614 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.652 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.58, V.59, T.60, W.253 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: G.67, N.69, S.242 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.117, T.119, N.120, V.122 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.144, W.147 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: E.127, N.160 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain B: R.452, E.460, R.461, D.462 Chain C: N.229 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.326, T.576 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.598 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.611, T.613, E.614 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.652 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: N.1093, T.1095, H.1096, F.1098 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