SMTL ID : 7r8m.1

Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C032

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

4 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: K.558 Chain B: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: N.714, F.715, L.919, N.922, Q.923 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.922, B:Q.923 Hydrogen bonds: B:Q.923 NAG-NAG.4: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.280, E.281, N.282 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: 10 residues within 4Å: Chain B: F.338, G.339, F.342, N.343, V.367, S.371 Chain F: R.59, Y.60, Q.65 Chain G: S.98 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:S.371, F:R.59, F:Y.60, F:Q.65

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

NAG.6: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.714 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: A.703, N.1071 Chain B: Q.892 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.1071 Chain C: Q.892 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: I.1129, N.1131 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain C: N.714, F.715, Q.923 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: I.1129, N.1131 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.460, K.462 Chain C: N.234, T.236 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: N.343 Chain D: R.59 Chain E: S.98 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: Q.892 Chain C: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: Y.351 Chain C: A.163, N.164, N.165 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
C032 Fab Heavy Chain: DF
C032 Fab Light Chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
H

E
E

G
L

Spike glycoprotein

C032 Fab Heavy Chain

C032 Fab Light Chain

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