SMTL ID : 8h7l.1

Cryo-EM Structure of SARS-CoV-2 BA.2 Spike protein in complex with BA7535

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.697, L.902, Q.906 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.902 NAG-NAG.3: 3 residues within 4Å: Chain A: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.311, Q.560 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.697, L.902, Q.906, Q.1051 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.902 NAG-NAG.7: 3 residues within 4Å: Chain B: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.311, Q.560 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.697, L.902, Q.906, Q.1051 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.902 NAG-NAG.11: 3 residues within 4Å: Chain C: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.311, Q.560 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.1114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1114 NAG.14: 2 residues within 4Å: Chain A: N.689 Chain C: I.774 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.689 NAG.15: 2 residues within 4Å: Chain A: A.686, N.1054 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain A: Y.635, V.636, N.637 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.635 NAG.17: 1 residues within 4Å: Chain B: N.1114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1114 NAG.18: 2 residues within 4Å: Chain A: Y.776 Chain B: N.689 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.689 NAG.19: 2 residues within 4Å: Chain B: A.686, N.1054 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1054 NAG.20: 4 residues within 4Å: Chain B: Y.635, V.636, N.637, K.676 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.637 NAG.21: 1 residues within 4Å: Chain C: N.1114 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1114 NAG.22: 2 residues within 4Å: Chain B: Y.776 Chain C: N.689 No protein-ligand interaction detected (PLIP) NAG.23: 2 residues within 4Å: Chain C: A.686, N.1054 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain C: Y.635, N.637 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Identification of a highly conserved neutralizing epitope within the RBD region of diverse SARS-CoV-2 variants. Nat Commun (2024)

Release Date

2023-08-30

Peptides

Spike glycoprotein: ABC
BA7535 fab heavt chain: DEF
BA7535 fab light chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

Spike glycoprotein

BA7535 fab heavt chain

BA7535 fab light chain

Related Entries With Identical Sequence