SMTL ID : 6xcn.1

Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-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: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: G.339, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: G.339, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: G.339, N.343, S.371 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925 NAG-NAG-BMA.8: 4 residues within 4Å: Chain B: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.922, B:N.925 NAG-NAG-BMA.13: 4 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.922, C:N.925

3 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.5: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.10: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.122, T.124, V.127 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.122, T.124, V.127 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.122, T.124, V.127 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell (2020)

Release Date

2020-07-01

Peptides

Spike glycoprotein: ABC
C105 Fab Heavy Chain: DEF
C105 Fab Light Chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
B

E
F

F
H

G
D

H
G

I
L

Spike glycoprotein

C105 Fab Heavy Chain

C105 Fab Light Chain

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