SMTL ID : 9ml5.1

Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-B8 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

9 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 A: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.714, F.715, L.919, Q.923 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.923 NAG-NAG.5: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.8: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.798, S.800 No protein-ligand interaction detected (PLIP)

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

NAG.10: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.122, T.124, N.125 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: E.309, N.603 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1071 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: G.339, F.342, N.343, F.374 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain B: K.558 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.1071 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: G.339, F.342, N.343 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.706 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1071 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: G.339, F.342, N.343 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Q.115, N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-06-04

Peptides

Spike glycoprotein: ABC
M8b-B8 heavy chain: DF
M8b-B8 light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
M

E
L

G
N

Spike glycoprotein

M8b-B8 heavy chain

M8b-B8 light chain

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