SMTL ID : 9ml7.1

Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C10 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

2 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.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.331, Q.580, T.581 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: V.615, N.616, Q.644 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: A.703, N.1071 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: T.307, N.603 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: D.793 Chain B: N.706, N.707, I.1127, G.1128 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.714, L.919 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: A.703, N.1071, F.1072 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: T.307, N.603 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: T.713, N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1071 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: I.1129, N.1131 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.281, N.282 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-C10 heavy chain: D
M8b-C10 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

M8b-C10 heavy chain

M8b-C10 light chain

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