SMTL ID : 7r8o.1

Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C548

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

5 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: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.714, L.919, N.922, Q.923 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.922 NAG-NAG.4: 3 residues within 4Å: Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.714, L.919, N.922, Q.923 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.922 NAG-NAG.7: 2 residues within 4Å: Chain B: N.798, Q.801 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 5 residues within 4Å: Chain A: G.339, N.343 Chain C: F.486 Chain F: A.101, G.103 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.103

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.5: 4 residues within 4Å: Chain A: F.486 Chain B: G.339, N.343 Chain H: A.101 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.8: 7 residues within 4Å: Chain B: F.486 Chain C: G.339, N.343 Chain D: E.100, A.101, Y.102, Y.111 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:N.343 Hydrogen bonds: D:E.100, D:A.101, D:Y.111, D:Y.111

26 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.9: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.616, C.617, T.618 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: K.558 Chain B: N.282 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: C.1079, N.1131 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.714, L.919 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.798, Q.801 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muecksch, F. et al., Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations. Immunity (2021)

Release Date

2021-08-04

Peptides

Spike glycoprotein: ABC
C548 Fab Heavy Chain: DFH
C548 Fab Light Chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
H

F
M

H
O

E
L

G
N

I
P

Spike glycoprotein

C548 Fab Heavy Chain

C548 Fab Light Chain

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