SMTL ID : 7wwj.1

SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab in the class 2 conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

14 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 C: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.2: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.703 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: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.15: 4 residues within 4Å: Chain A: Y.28, N.30, F.59, N.61 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.231 Chain B: H.516 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain B: K.555 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.328, L.579 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: T.106, T.107, N.231, T.233 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: E.278, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: Y.793 Chain B: N.706 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.231 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: K.555 Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.793 Chain C: N.706 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, H. et al., EM structure of SARS-CoV-2 Omicron variant spike glycoprotein and 55A8. To Be Published

Release Date

2023-02-15

Peptides

Spike glycoprotein: ABC
55A8 light chain: DF
55A8 heavy chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

F
H

E
G

G
I

Spike glycoprotein

55A8 light chain

55A8 heavy chain

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